| Ordo | Keluarga | Jenis | Occurrence | Nama FishBase | Name(s) in Territory |
|---|---|---|---|---|---|
| Tetraodontiformes | Balistidae | Abalistes stellatus | native | Starry triggerfish | Japanese : Okihagi |
| Lophiiformes | Antennariidae | Abantennarius analis | native | Tailjet frogfish | |
| Lophiiformes | Antennariidae | Abantennarius coccineus | native | Scarlet frogfish | Japanese : Gomafu-izariuo |
| Lophiiformes | Antennariidae | Abantennarius dorehensis | native | New Guinean frogfish | Japanese : Kasuri-izari-ou |
| Lophiiformes | Antennariidae | Abantennarius nummifer | native | Spotfin frogfish | Japanese : Beni-izariuo; Japanese : Nihon-izariuo; |
| Cypriniformes | Gobionidae | Abbottina rivularis | native | Chinese false gudgeon | Japanese : Tsuchifuki |
| Perciformes/Scorpaenoidei | Tetrarogidae | Ablabys gymnothorax | native | Scaleless spiny waspfsh | Japanese : Kasasa-haokoze |
| Perciformes/Scorpaenoidei | Tetrarogidae | Ablabys taenianotus | native | Cockatoo waspfish | Japanese : Tsumajiro-okoze |
| Beloniformes | Belonidae | Ablennes hians | native | Flat needlefish | Japanese : Hama-datsu |
| Ovalentaria/misc | Pomacentridae | Abudefduf bengalensis | native | Bengal sergeant | Japanese : Tenjiku-suzumedai |
| Ovalentaria/misc | Pomacentridae | Abudefduf lorenzi | native | Black-tail sergeant | |
| Ovalentaria/misc | Pomacentridae | Abudefduf notatus | native | Yellowtail sergeant | Japanese : Iso-suzumedai |
| Ovalentaria/misc | Pomacentridae | Abudefduf septemfasciatus | native | Banded sergeant | Japanese : Shichisen-suzumedai |
| Ovalentaria/misc | Pomacentridae | Abudefduf sexfasciatus | native | Scissortail sergeant | Japanese : Rokusen-suzumedai |
| Ovalentaria/misc | Pomacentridae | Abudefduf sordidus | native | Blackspot sergeant | Japanese : Shima-suzumedai |
| Ovalentaria/misc | Pomacentridae | Abudefduf vaigiensis | native | Indo-Pacific sergeant | Japanese : Oyabiccha |
| Acropomatiformes | Hemerocoetidae | Acanthaphritis barbata | native | Japanese : Higetoragisu | |
| Acropomatiformes | Hemerocoetidae | Acanthaphritis unoorum | native | ||
| Eupercaria/misc | Cepolidae | Acanthocepola krusensternii | native | Red-spotted bandfish | Japanese : Akatachi |
| Eupercaria/misc | Cepolidae | Acanthocepola limbata | native | Blackspot bandfish | Japanese : Itten-akatachi |
| Scombriformes | Scombridae | Acanthocybium solandri | native | Wahoo | Japanese : Kamasu-sawara |
| Gobiiformes | Gobiidae | Acanthogobius flavimanus | native | Yellowfin goby | Japanese : Mahaze |
| Gobiiformes | Gobiidae | Acanthogobius hasta | native | Japanese : Hazekuchi | |
| Gobiiformes | Gobiidae | Acanthogobius insularis | native | ||
| Gobiiformes | Gobiidae | Acanthogobius lactipes | native | Japanese : Ashishirohaze | |
| Perciformes/Zoarcoidei | Lumpenidae | Acantholumpenus mackayi | native | Pighead prickleback | Japanese : Nuimegaji |
| Ophidiiformes | Ophidiidae | Acanthonus armatus | native | Bony-eared assfish | Japanese : Hanatoge-ashiro |
| Eupercaria/misc | Sparidae | Acanthopagrus chinshira | native | Okinawan yellow-fin seabream | Japanese : Okinawa-kichinu |
| Eupercaria/misc | Sparidae | Acanthopagrus latus | native | Yellowfin seabream | Japanese : Kichinu |
| Eupercaria/misc | Sparidae | Acanthopagrus pacificus | native | Pacific seabream | Japanese : Nan'yo-chinu; Japanese : Nanyôchinu; |
| Eupercaria/misc | Sparidae | Acanthopagrus schlegelii | native | Blackhead seabream | Japanese : Kurodai |
| Ovalentaria/misc | Plesiopidae | Acanthoplesiops hiatti | native | Hiatt's basslet | |
| Ovalentaria/misc | Plesiopidae | Acanthoplesiops psilogaster | native | Barebelly longfin | Japanese : Fuchidori-tanabata-uo |
| Pleuronectiformes | Pleuronectidae | Acanthopsetta nadeshnyi | native | Scale-eye plaice | Japanese : Urokomegarei |
| Acanthuriformes | Acanthuridae | Acanthurus achilles | native | Achilles tang | |
| Acanthuriformes | Acanthuridae | Acanthurus bariene | native | Blackspot surgeonfish | Japanese : Kanranhagi |
| Acanthuriformes | Acanthuridae | Acanthurus blochii | native | Ringtail surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus dussumieri | native | Eyestripe surgeonfish | Japanese : Nise-kanranhagi |
| Acanthuriformes | Acanthuridae | Acanthurus guttatus | native | Whitespotted surgeonfish | Japanese : Gomaniza |
| Acanthuriformes | Acanthuridae | Acanthurus japonicus | native | Japan surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus leucopareius | native | Whitebar surgeonfish | Japanese : Suji-kurohagi |
| Acanthuriformes | Acanthuridae | Acanthurus lineatus | native | Lined surgeonfish | Japanese : Nijihagi |
| Acanthuriformes | Acanthuridae | Acanthurus maculiceps | native | White-freckled surgeonfish | Japanese : Irezuminiza |
| Acanthuriformes | Acanthuridae | Acanthurus mata | native | Elongate surgeonfish | Japanese : Hiraniza |
| Acanthuriformes | Acanthuridae | Acanthurus nigricans | native | Whitecheek surgeonfish | Japanese : Megane-kurohagi |
| Acanthuriformes | Acanthuridae | Acanthurus nigricauda | native | Epaulette surgeonfish | |
| Acanthuriformes | Acanthuridae | Acanthurus nigrofuscus | native | Brown surgeonfish | Japanese : Naganiza |
| Acanthuriformes | Acanthuridae | Acanthurus olivaceus | native | Orangespot surgeonfish | Japanese : Montsukihagi |
| Acanthuriformes | Acanthuridae | Acanthurus pyroferus | native | Mimic surgeonfish | Japanese : Kuroguchiniza |
| Acanthuriformes | Acanthuridae | Acanthurus thompsoni | native | Thompson's surgeonfish | Japanese : Ohagurohagi |
| Acanthuriformes | Acanthuridae | Acanthurus triostegus | native | Convict surgeonfish | Japanese : Shimahagi |
| Acanthuriformes | Acanthuridae | Acanthurus xanthopterus | native | Yellowfin surgeonfish | Japanese : Kurohagi |
| Gobiiformes | Gobiidae | Acentrogobius audax | native | Mangrove goby | Japanese : Nisetsumugihaze |
| Gobiiformes | Gobiidae | Acentrogobius caninus | native | Tropical sand goby | |
| Gobiiformes | Gobiidae | Acentrogobius janthinopterus | native | Robust mangrove goby | Japanese : Kasumihaze |
| Gobiiformes | Gobiidae | Acentrogobius moloanus | native | Barcheek Amoya | Japanese : Futasujinoborihaze |
| Gobiiformes | Gobiidae | Acentrogobius multifasciatus | native | Japanese : Seitaka-sujihaze | |
| Gobiiformes | Gobiidae | Acentrogobius nebulosus | native | Shadow goby | Japanese : Tsumugihaze |
| Gobiiformes | Gobiidae | Acentrogobius pflaumii | native | Striped sandgoby | Japanese : Sujihaze |
| Gobiiformes | Gobiidae | Acentrogobius suluensis | native | Sulu goby | Japanese : Hohoguro-sujihaze |
| Gobiiformes | Gobiidae | Acentrogobius viganensis | native | Japanese : Suzumehaze | |
| Gobiiformes | Gobiidae | Acentrogobius viridipunctatus | native | Spotted green goby | Japanese : Kirarahaze |
| Syngnathiformes | Syngnathidae | Acentronura gracilissima | native | Bastard seahorse | Japanese : Tatsunoitoko |
| Cypriniformes | Acheilognathidae | Acheilognathus coreanus | native | ||
| Cypriniformes | Acheilognathidae | Acheilognathus cyanostigma | native | Striped bitterling | Japanese : Ichimonjitanago |
| Cypriniformes | Acheilognathidae | Acheilognathus intermedia | native | ||
| Cypriniformes | Acheilognathidae | Acheilognathus longipinnis | native | Deepbody bitterling | Japanese : Itasenpara |
| Cypriniformes | Acheilognathidae | Acheilognathus macropterus | introduced | ||
| Cypriniformes | Acheilognathidae | Acheilognathus melanogaster | native | Japanese : Tanago | |
| Cypriniformes | Acheilognathidae | Acheilognathus rhombeus | native | Japanese : Kanehira | |
| Cypriniformes | Acheilognathidae | Acheilognathus tabira | native | English : Red tabira bitterling; English : Southern red tabira bitterling; | |
| Cypriniformes | Acheilognathidae | Acheilognathus typus | native | Japanese : Zenitanago | |
| Acipenseriformes | Acipenseridae | Acipenser mikadoi | native | Sakhalin sturgeon | Japanese : Chôzame |
| Acipenseriformes | Acipenseridae | Acipenser schrenckii | native | Amur sturgeon | Japanese : Amûru-chôzame; Japanese : Sennin-chôzame; |
| Acipenseriformes | Acipenseridae | Acipenser sinensis | native | Chinese sturgeon | Japanese : Kara-chôzame |
| Tetraodontiformes | Monacanthidae | Acreichthys hajam | native | Japanese : Togekawahagi | |
| Tetraodontiformes | Monacanthidae | Acreichthys radiatus | native | Radial leatherjacket | Japanese : Sudarekawahagi |
| Tetraodontiformes | Monacanthidae | Acreichthys tomentosus | native | Bristle-tail file-fish | Japanese : Fuchidorikawahagi |
| Anguilliformes | Congridae | Acromycter nezumi | native | Japanese : Himo-anago | |
| Acropomatiformes | Acropomatidae | Acropoma hanedai | native | Japanese : Haneda-hotarujako | |
| Acropomatiformes | Acropomatidae | Acropoma japonicum | native | Glowbelly | Japanese : Hotarujako |
| Acropomatiformes | Acropomatidae | Acropoma lecorneti | native | Lecornet's lanternbelly | Japanese : オキナワホタルジャコ |
| Syngnathiformes | Centriscidae | Aeoliscus strigatus | native | Jointed Razorfish | Japanese : Heko-ayu |
| Pleuronectiformes | Soleidae | Aesopia cornuta | native | Unicorn sole | Japanese : Tsuno-ushinoshita |
| Perciformes/Serranoidei | Epinephelidae | Aethaloperca rogaa | native | Redmouth grouper | Japanese : Kurohata |
| Myliobatiformes | Aetobatidae | Aetobatus narutobiei | native | Naru eagle ray | |
| Myliobatiformes | Aetobatidae | Aetobatus ocellatus | native | Ocellated eagle ray | |
| Myliobatiformes | Myliobatidae | Aetomylaeus nichofii | native | Banded eagle ray | Japanese : Aosuji-tobi-ei |
| Perciformes/Cottoidei | Agonidae | Agonomalus jordani | native | Japanese : Kumagai-uo | |
| Perciformes/Cottoidei | Agonidae | Agonomalus proboscidalis | native | Japanese : Atsumori-uo | |
| Aulopiformes | Notosudidae | Ahliesaurus brevis | native | Japanese : Fukami-fude-eso | |
| Gadiformes | Macrouridae | Albatrossia pectoralis | native | Giant grenadier | Japanese : Munedara |
| Albuliformes | Albulidae | Albula argentea | native | Longjaw bonefish | |
| Albuliformes | Albulidae | Albula glossodonta | native | Roundjaw bonefish | |
| Albuliformes | Albulidae | Albula vulpes | native | Bonefish | Japanese : Soto-iwashi |
| Perciformes/Cottoidei | Cottidae | Alcichthys elongatus | native | Japanese : Kama-bero; Japanese : Niji-kajika; Japanese : Nijikajika; | |
| Ophidiiformes | Ophidiidae | Alcockia rostrata | native | ||
| Notacanthiformes | Halosauridae | Aldrovandia affinis | native | Gilbert's halosaurid fish | Japanese : Tokagegisu |
| Carangiformes | Carangidae | Alectis ciliaris | native | African pompano | Japanese : Itohiki-aji |
| Perciformes/Zoarcoidei | Stichaeidae | Alectrias alectrolophus | native | Stone cockscomb | Japanese : Kita-mushaginpo |
| Perciformes/Zoarcoidei | Stichaeidae | Alectrias benjamini | native | Spiny cockscomb | Japanese : Mushaginpo |
| Perciformes/Zoarcoidei | Stichaeidae | Alectrias markevichi | native | English : Slender cockscomb | |
| Perciformes/Zoarcoidei | Stichaeidae | Alectrias mutsuensis | native | Maned cockscomb | Japanese : Mutsu-musha-ginpo |
| Carangiformes | Carangidae | Alepes djedaba | native | Shrimp scad | Japanese : Tsumari-mabuta-aji |
| Carangiformes | Carangidae | Alepes kleinii | native | Razorbelly scad | Japanese : Miyakamihira-aji |
| Carangiformes | Carangidae | Alepes melanoptera | native | Blackfin scad | Japanese : Seguro-mabuta-aji |
| Carangiformes | Carangidae | Alepes vari | native | Herring scad | Japanese : Mabutashima-aji |
| Aulopiformes | Alepisauridae | Alepisaurus ferox | native | Long snouted lancetfish | Japanese : Mizu-uo |
| Alepocephaliformes | Alepocephalidae | Alepocephalus bicolor | native | Bicolor slickhead | Japanese : Hosome-konnyaku-iwashi |
| Alepocephaliformes | Alepocephalidae | Alepocephalus longiceps | native | Longfin slickhead | Japanese : Togari-konnyaku-iwashi |
| Alepocephaliformes | Alepocephalidae | Alepocephalus owstoni | native | Owston's slickhead | Japanese : Hage-iwashi |
| Alepocephaliformes | Alepocephalidae | Alepocephalus umbriceps | native | Slickhead | Japanese : Konnyaku-iwashi |
| Ophidiiformes | Dinematichthyidae | Alionematichthys piger | native | Whiskered viviparous brotula | |
| Ophidiiformes | Dinematichthyidae | Alionematichthys riukiuensis | native | Bigeye cusk | Japanese : Ryukyu-itachiuo |
| Perciformes/Cottoidei | Liparidae | Allocareproctus jordani | native | Cherry snailfish | Japanese : Misaki-bikunin |
| Zeiformes | Oreosomatidae | Allocyttus folletti | native | Oxeye oreo | |
| Lamniformes | Alopiidae | Alopias pelagicus | native | Pelagic thresher | Japanese : Nitari |
| Lamniformes | Alopiidae | Alopias superciliosus | native | Bigeye thresher | Japanese : Hachiware |
| Lamniformes | Alopiidae | Alopias vulpinus | native | Thresher | Japanese : Mao-naga |
| Blenniiformes | Blenniidae | Alticus orientalis | native | ||
| Blenniiformes | Blenniidae | Alticus saliens | native | Leaping blenny | Japanese : Tamakaeru-uo |
| Tetraodontiformes | Monacanthidae | Aluterus monoceros | native | Unicorn leatherjacket filefish | Japanese : Usubahagi |
| Tetraodontiformes | Monacanthidae | Aluterus scriptus | native | Scrawled Filefish | Japanese : Sôshihagi |
| Eupercaria/misc | Sparidae | Amamiichthys matsubarai | native | Japanese blue-spotted seabream | Japanese : Hoshirenko |
| Tetraodontiformes | Monacanthidae | Amanses scopas | native | Broom filefish | Japanese : Azamikawahagi |
| Scombriformes | Amarsipidae | Amarsipus carlsbergi | native | Amarsipa | Japanese : Tokonatsu-ibodai |
| Cichliformes | Cichlidae | Amatitlania nigrofasciata | introduced | Convict cichlid | |
| Ovalentaria/misc | Ambassidae | Ambassis buruensis | native | Buru glass perchlet | Japanese : Togenaga-takasago-ishimochi |
| Ovalentaria/misc | Ambassidae | Ambassis interrupta | native | Long-spined glass perchlet | Japanese : Nanyô-takasago-ishimochi |
| Ovalentaria/misc | Ambassidae | Ambassis miops | native | Flag-tailed glass perchlet | Japanese : Sesuji-takasago-ishimochi |
| Ovalentaria/misc | Ambassidae | Ambassis urotaenia | native | Banded-tail glassy perchlet | Japanese : Takasago-ishimochi |
| Gobiiformes | Gobiidae | Amblychaeturichthys hexanema | native | Japanese : Akahaze | |
| Gobiiformes | Gobiidae | Amblychaeturichthys sciistius | native | Japanese : Komochijako | |
| Centrarchiformes | Cirrhitidae | Amblycirrhitus bimacula | native | Twospot hawkfish | |
| Centrarchiformes | Cirrhitidae | Amblycirrhitus unimacula | native | Japanese : Kurohoshigonbe | |
| Gobiiformes | Gobiidae | Amblyeleotris fasciata | native | Red-banded prawn-goby | Japanese : Kubiakahaze |
| Gobiiformes | Gobiidae | Amblyeleotris guttata | native | Spotted prawn-goby | Japanese : Yamabukihaze |
| Gobiiformes | Gobiidae | Amblyeleotris japonica | native | Japanese : Datehaze | |
| Gobiiformes | Gobiidae | Amblyeleotris masuii | native | Masui's shrimp-goby | Japanese : Masui-datehaze |
| Gobiiformes | Gobiidae | Amblyeleotris melanocephala | native | Blackhead shrimpgoby | Japanese : Zuguro-datehaze |
| Gobiiformes | Gobiidae | Amblyeleotris morishitai | native | Japanese : Morishita-datehaze | |
| Gobiiformes | Gobiidae | Amblyeleotris ogasawarensis | native | Redspotted shrimpgoby | Japanese : Minami-datehaze |
| Gobiiformes | Gobiidae | Amblyeleotris periophthalma | native | Periophthalma prawn-goby | Japanese : Dandara-datehaze |
| Gobiiformes | Gobiidae | Amblyeleotris randalli | native | Randall's prawn-goby | |
| Gobiiformes | Gobiidae | Amblyeleotris steinitzi | native | Steinitz' prawn-goby | Japanese : Hime-datehaze |
| Gobiiformes | Gobiidae | Amblyeleotris wheeleri | native | Gorgeous prawn-goby | |
| Clupeiformes | Dorosomatidae | Amblygaster clupeoides | native | Bleeker smoothbelly sardinella | |
| Clupeiformes | Dorosomatidae | Amblygaster leiogaster | native | Smoothbelly sardinella | Japanese : Yamato-mizun |
| Clupeiformes | Dorosomatidae | Amblygaster sirm | native | Spotted sardinella | Japanese : Hoshi-yamato-mizun |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon aureus | native | Golden damselfish | Japanese : Yamabuki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon curacao | native | Staghorn damselfish | Japanese : Kurakao-suzumedai |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon leucogaster | native | Yellowbelly damselfish | Japanese : Nami-suzumedai |
| Ovalentaria/misc | Pomacentridae | Amblyglyphidodon ternatensis | native | Ternate damsel | Japanese : Nise-kurakao-suzumedai |
| Gobiiformes | Gobiidae | Amblygobius albimaculatus | native | Butterfly goby | Japanese : Sarasahaze |
| Gobiiformes | Gobiidae | Amblygobius cheraphilus | native | East Indies siltgoby | |
| Gobiiformes | Gobiidae | Amblygobius decussatus | native | Orange-striped goby | Japanese : Jûmonji-sarasahaze |
| Gobiiformes | Gobiidae | Amblygobius linki | native | Link's goby | Japanese : Wakake-sarasahaze |
| Gobiiformes | Gobiidae | Amblygobius nocturnus | native | Nocturn goby | Japanese : Hohobeni-sarasahaze |
| Gobiiformes | Gobiidae | Amblygobius phalaena | native | Whitebarred goby | |
| Gobiiformes | Gobiidae | Amblygobius sphynx | native | Sphinx goby | |
| Ovalentaria/misc | Pomacentridae | Amblypomacentrus tricinctus | native | Threeband damselfish | Japanese : Misuji suzumedai |
| Rajiformes | Rajidae | Amblyraja hyperborea | native | Arctic skate | |
| Kurtiformes | Apogonidae | Amioides polyacanthus | native | Japanese : Oni-ishimochi | |
| Perciformes/Uranoscopoidei | Ammodytidae | Ammodytes heian | native | Peaceful sand lance | Japanese : Oh-ikanago |
| Perciformes/Uranoscopoidei | Ammodytidae | Ammodytes hexapterus | native | Pacific sand lance | Japanese : Kita-ikaanago |
| Perciformes/Uranoscopoidei | Ammodytidae | Ammodytes personatus | native | Pacific sandlance | |
| Perciformes/Uranoscopoidei | Ammodytidae | Ammodytoides kanazawai | native | Japanese : Gomahire-minami-ikanago | |
| Perciformes/Uranoscopoidei | Ammodytidae | Ammodytoides kimurai | native | ||
| Ovalentaria/misc | Pomacentridae | Amphiprion clarkii | native | Yellowtail clownfish | Japanese : Kumanomi |
| Ovalentaria/misc | Pomacentridae | Amphiprion frenatus | native | Tomato clownfish | Japanese : Hama-kumanomi |
| Ovalentaria/misc | Pomacentridae | Amphiprion ocellaris | native | Clown anemonefish | Japanese : Kakure-kumanomi |
| Ovalentaria/misc | Pomacentridae | Amphiprion perideraion | native | Pink anemonefish | Japanese : Hanabira-kumanomi |
| Ovalentaria/misc | Pomacentridae | Amphiprion polymnus | native | Saddleback clownfish | Japanese : Tôaka-kumanomi |
| Ovalentaria/misc | Pomacentridae | Amphiprion sandaracinos | native | Yellow clownfish | Japanese : Sejiro-kumanomi |
| Eupercaria/misc | Labridae | Anampses caeruleopunctatus | native | Bluespotted wrasse | Japanese : Buchi-susukibera |
| Eupercaria/misc | Labridae | Anampses geographicus | native | Geographic wrasse | Japanese : Mushibera |
| Eupercaria/misc | Labridae | Anampses melanurus | native | White-spotted wrasse | Japanese : Kurofuchi-susukibera |
| Eupercaria/misc | Labridae | Anampses meleagrides | native | Spotted wrasse | Japanese : Hokutobera |
| Eupercaria/misc | Labridae | Anampses neoguinaicus | native | New Guinea wrasse | Japanese : Nyûginiabera |
| Eupercaria/misc | Labridae | Anampses twistii | native | Yellowbreasted wrasse | Japanese : Hoshi-susukibera |
| Callionymiformes | Callionymidae | Anaora tentaculata | native | Tentacled dragonet | Japanese : Tanzaku-teguri |
| Anguilliformes | Muraenidae | Anarchias seychellensis | native | Seychelles moray | |
| Perciformes/Zoarcoidei | Anarhichadidae | Anarhichas orientalis | native | Bering wolffish | Japanese : Ôkami-uo |
| Perciformes/Zoarcoidei | Anarhichadidae | Anarrhichthys ocellatus | native | Wolf-eel | |
| Gobiiformes | Gobiidae | Ancistrogobius dipus | native | Double-fin cheek-hook goby | Japanese : Futahire ho'okagi-haze |
| Gobiiformes | Gobiidae | Ancistrogobius squamiceps | native | Scaly cheek-hook goby | Japanese : Uroko ho'okagi-haze |
| Gobiiformes | Gobiidae | Ancistrogobius yanoi | native | Yano's cheek-hook goby | Japanese : Asabano ho'okagi-haze |
| Gobiiformes | Gobiidae | Ancistrogobius yoshigoui | native | Threadless cheek-hook goby | Japanese : Itokake Ho'okagi-haze |
| Blenniiformes | Blenniidae | Andamia pacifica | native | ||
| Blenniiformes | Blenniidae | Andamia reyi | native | Suckerlip blenny | |
| Blenniiformes | Blenniidae | Andamia tetradactylus | native | Four-fingered lipsucker | Japanese : Yodarekake |
| Perciformes/Zoarcoidei | Zoarcidae | Andriashevia aptera | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Andriashevia natsushimae | endemic | Japanese : Natsushimachojyagenge | |
| Anguilliformes | Anguillidae | Anguilla bicolor | native | Indonesian shortfin eel | |
| Anguilliformes | Anguillidae | Anguilla japonica | native | Japanese eel | Japanese : Unagi |
| Anguilliformes | Anguillidae | Anguilla marmorata | native | Giant mottled eel | Japanese : Ô-unagi |
| Perciformes/Zoarcoidei | Lumpenidae | Anisarchus macrops | native | Japanese : Medamaginpo | |
| Perciformes/Zoarcoidei | Lumpenidae | Anisarchus medius | native | Stout eelblenny | |
| Trachichthyiformes | Anomalopidae | Anomalops katoptron | native | Splitfin flashlightfish | |
| Perciformes/Cottoidei | Agonidae | Anoplagonus occidentalis | native | Japanese : Nise-nametokubire | |
| Trachichthyiformes | Anoplogastridae | Anoplogaster cornuta | native | Common fangtooth | Japanese : Onikinme |
| Perciformes/Cottoidei | Anoplopomatidae | Anoplopoma fimbria | native | Sablefish | Japanese : Gindara |
| Aulopiformes | Anotopteridae | Anotopterus nikparini | native | North Pacific daggertooth | Japanese : Mizu-uodamashi |
| Rhinopristiformes | Pristidae | Anoxypristis cuspidata | native | Pointed sawfish | Japanese : Nokogiri-ei |
| Lophiiformes | Antennariidae | Antennarius commerson | native | Commerson's frogfish | Japanese : Oni izariuo |
| Lophiiformes | Antennariidae | Antennarius pictus | native | Painted frogfish | Japanese : Ômon-izariuo |
| Lophiiformes | Antennariidae | Antennarius randalli | native | Randall's frogfish | |
| Lophiiformes | Antennariidae | Antennarius striatus | native | Striated frogfish | Japanese : Izariuo |
| Lophiiformes | Antennariidae | Antennatus flagellatus | endemic | Japanese : Muchi-izari-uo | |
| Acanthuriformes | Antigoniidae | Antigonia capros | native | Deepbody boarfish | Japanese : Hishidai |
| Acanthuriformes | Antigoniidae | Antigonia rubescens | native | Indo-Pacific boarfish | Japanese : Beni-hishidai |
| Gadiformes | Moridae | Antimora microlepis | native | Finescale mora | Japanese : Kanada-dara |
| Perciformes/Serranoidei | Epinephelidae | Anyperodon leucogrammicus | native | Slender grouper | Japanese : Azukihata |
| Scombriformes | Trichiuridae | Aphanopus arigato | native | Pacific black scabbardfish | Japanese : Kurotachimodoki |
| Eupercaria/misc | Lutjanidae | Aphareus furca | native | Small toothed jobfish | Japanese : Ishifuedai |
| Eupercaria/misc | Lutjanidae | Aphareus rutilans | native | Rusty jobfish | Japanese : Ôguchi-ishichibiki |
| Cypriniformes | Xenocyprididae | Aphyocypris chinensis | native | Chinese bleak | Japanese : Hinamoroko |
| Ophidiiformes | Bythitidae | Aphyonus gelatinosus | native | Gelatinous blindfish | |
| Perciformes/Scorpaenoidei | Apistidae | Apistus carinatus | native | Ocellated waspfish | Japanese : Hachi |
| Perciformes/Scorpaenoidei | Aploactinidae | Aploactis aspera | native | Dusky velvetfish | Japanese : Ibo-okoze |
| Gobiiformes | Oxudercidae | Apocryptodon madurensis | native | Madura goby | Japanese : Tabirakuchi |
| Gobiiformes | Oxudercidae | Apocryptodon punctatus | native | Japanese : Tabirakuchi | |
| Kurtiformes | Apogonidae | Apogon coccineus | native | Ruby cardinalfish | Japanese : Kominato-tenjikudai |
| Kurtiformes | Apogonidae | Apogon crassiceps | native | Transparent cardinalfish | Japanese : Akane-tenjikudai |
| Kurtiformes | Apogonidae | Apogon doryssa | native | Longspine cardinalfish | Japanese : Yari-ishimochi |
| Kurtiformes | Apogonidae | Apogon seminigracaudus | native | Darktail cardinalfish | Japanese : Oguro-tenjikudai |
| Kurtiformes | Apogonidae | Apogon semiornatus | native | Oblique-banded cardinalfish | Japanese : Yami-tenjikudai |
| Kurtiformes | Apogonidae | Apogon unicolor | native | Big red cardinalfish | Japanese : Hana-ishimochi |
| Kurtiformes | Apogonidae | Apogonichthyoides cathetogramma | native | Japanese : Yokosuji-ishimochi | |
| Kurtiformes | Apogonidae | Apogonichthyoides melas | native | Black cardinalfish | Japanese : Montsuki-ishimochi |
| Kurtiformes | Apogonidae | Apogonichthyoides niger | native | Japanese : Kuro-ishimochi | |
| Kurtiformes | Apogonidae | Apogonichthyoides pseudotaeniatus | native | Doublebar cardinalfish | |
| Kurtiformes | Apogonidae | Apogonichthyoides sialis | native | Twinbar cardinalfish | |
| Kurtiformes | Apogonidae | Apogonichthyoides timorensis | native | Timor cardinalfish | Japanese : Kakure-ishimochi |
| Kurtiformes | Apogonidae | Apogonichthys ocellatus | native | Ocellate cardinalfish | Japanese : Mato-shibori |
| Kurtiformes | Apogonidae | Apogonichthys perdix | native | Perdix cardinalfish | Japanese : Hawai-mato-ishimochi |
| Acanthuriformes | Pomacanthidae | Apolemichthys trimaculatus | native | Threespot angelfish | Japanese : Shiten-yakko |
| Perciformes/Serranoidei | Grammistidae | Aporops bilinearis | native | Blotched podge | Japanese : Nanyo-togemegisu |
| Eupercaria/misc | Lutjanidae | Aprion virescens | native | Green jobfish | Japanese : Aochibiki |
| Carcharhiniformes | Pentanchidae | Apristurus fedorovi | native | ||
| Carcharhiniformes | Pentanchidae | Apristurus herklotsi | native | Longfin catshark | |
| Carcharhiniformes | Pentanchidae | Apristurus japonicus | native | Japanese catshark | Japanese : Nihon-herazame |
| Carcharhiniformes | Pentanchidae | Apristurus longicephalus | native | Longhead catshark | Japanese : Tengu-herazame |
| Carcharhiniformes | Pentanchidae | Apristurus macrorhynchus | native | Flathead catshark | Japanese : Naga-herazame |
| Carcharhiniformes | Pentanchidae | Apristurus platyrhynchus | native | Borneo catshark | Japanese : Herazame |
| Anguilliformes | Ophichthidae | Apterichtus australis | native | Snake eel | |
| Anguilliformes | Ophichthidae | Apterichtus hatookai | native | Orange blotched eel | Japanese : Daidai-madara-umihebi |
| Anguilliformes | Ophichthidae | Apterichtus moseri | endemic | Japanese : Goma-umihebi | |
| Anguilliformes | Ophichthidae | Apterichtus orientalis | native | Japanese : Kishu-goma-umihebi | |
| Anguilliformes | Ophichthidae | Apterichtus soyoae | native | Japanese : Soyo-goma-umihebi | |
| Perciformes/Cottoidei | Cyclopteridae | Aptocyclus ventricosus | native | Smooth lumpsucker | Japanese : Hotei-uo |
| Rajiformes | Arhynchobatidae | Arctoraja parmifera | native | Alaska skate | |
| Rajiformes | Arhynchobatidae | Arctoraja simoterus | native | Hokkaido skate | Japanese : Tsunokasube |
| Perciformes/Uranoscopoidei | Trichodontidae | Arctoscopus japonicus | native | Japanese sandfish | Japanese : Hatahata |
| Aulopiformes | Paralepididae | Arctozenus risso | native | Spotted barracudina | Japanese : Hikari-eso |
| Gobiiformes | Gobiidae | Arcygobius baliurus | native | Isthmus goby | Japanese : Tongarihaze |
| Argentiniformes | Argentinidae | Argentina kagoshimae | native | Japanese : Kagoshima-nigisu | |
| Perciformes/Cottoidei | Cottidae | Argyrocottus zanderi | native | Japanese : Itohikikajika | |
| Stomiiformes | Sternoptychidae | Argyropelecus aculeatus | native | Lovely hatchetfish | Japanese : Togarimune-eso |
| Stomiiformes | Sternoptychidae | Argyropelecus affinis | native | Pacific hatchet fish | Japanese : Naga-mune-eso |
| Stomiiformes | Sternoptychidae | Argyropelecus hemigymnus | native | Half-naked hatchetfish | Japanese : Tengan-mune-eso |
| Stomiiformes | Sternoptychidae | Argyropelecus sladeni | native | Sladen's hatchet fish | Japanese : Te-ono-eso |
| Eupercaria/misc | Sparidae | Argyrops bleekeri | native | Taiwan tai | Japanese : Taiwandai |
| Eupercaria/misc | Sciaenidae | Argyrosomus japonicus | native | Japanese meagre | Japanese : Ô-nibe |
| Scombriformes | Ariommatidae | Ariomma brevimanus | native | Japanese : Minami-medai; Japanese : Naga-medai; | |
| Scombriformes | Ariommatidae | Ariomma indica | native | Indian driftfish | Japanese : Maru-ibodai |
| Scombriformes | Ariommatidae | Ariomma lurida | native | Ariommid | Japanese : Ôme-medai |
| Anguilliformes | Congridae | Ariosoma anago | native | Silvery conger | Japanese : Goten-anago |
| Anguilliformes | Congridae | Ariosoma anagoides | native | Sea conger | Japanese : Hana-anago |
| Anguilliformes | Congridae | Ariosoma dolichopterum | native | Long-fin short-tail conger | |
| Anguilliformes | Congridae | Ariosoma majus | native | Major short-tail conger | Japanese : Ôshiro-anago |
| Anguilliformes | Congridae | Ariosoma meeki | native | Meek's short-tail conger | |
| Anguilliformes | Congridae | Ariosoma shiroanago | native | White short-tail conger | Japanese : Shiro-anago |
| Siluriformes | Ariidae | Arius maculatus | native | Spotted catfish | Japanese : Hamagigi |
| Pleuronectiformes | Bothidae | Arnoglossus japonicus | native | Japanese lefteye flounder | Japanese : Nihon-darumagarei |
| Pleuronectiformes | Bothidae | Arnoglossus macrolophus | native | Large-crested lefteye flounder | Japanese : Niten-nagadarumagarei |
| Pleuronectiformes | Bothidae | Arnoglossus oxyrhynchus | native | Sharp-snout lefteye flounder | Japanese : Hanatogodarumagarei |
| Pleuronectiformes | Bothidae | Arnoglossus polyspilus | native | Many-spotted lefteye flounder | Japanese : Nanyôdarumagarei |
| Pleuronectiformes | Bothidae | Arnoglossus tenuis | native | Dwarf lefteye flounder | Japanese : Nagadarumagarei |
| Tetraodontiformes | Tetraodontidae | Arothron caeruleopunctatus | native | Blue-spotted puffer | Japanese : Arare-fugu |
| Tetraodontiformes | Tetraodontidae | Arothron firmamentum | native | Starry toado | Japanese : Hoshifugu |
| Tetraodontiformes | Tetraodontidae | Arothron hispidus | native | White-spotted puffer | Japanese : Sazanamifugu |
| Tetraodontiformes | Tetraodontidae | Arothron immaculatus | native | Immaculate puffer | Japanese : Kasumifugu |
| Tetraodontiformes | Tetraodontidae | Arothron manilensis | native | Narrowlined puffer | Japanese : Suji-moyôfugu |
| Tetraodontiformes | Tetraodontidae | Arothron mappa | native | Map puffer | Japanese : Keshôfugu |
| Tetraodontiformes | Tetraodontidae | Arothron meleagris | native | Guineafowl puffer | Japanese : Mizorefugu |
| Tetraodontiformes | Tetraodontidae | Arothron multilineatus | native | Many-lined pufferfish | Japanese : Tasuji-fugu |
| Tetraodontiformes | Tetraodontidae | Arothron nigropunctatus | native | Blackspotted puffer | Japanese : Kokutenfugu |
| Tetraodontiformes | Tetraodontidae | Arothron reticularis | native | Reticulated pufferfish | Japanese : Wamonfugu |
| Tetraodontiformes | Tetraodontidae | Arothron stellatus | native | Stellate puffer | Japanese : Moyôfugu |
| Perciformes/Cottoidei | Cottidae | Artediellus camchaticus | native | Japanese : Kamuchakkakajika | |
| Perciformes/Cottoidei | Cottidae | Artediellus dydymovi | native | Japanese : Kobu-okikajika | |
| Perciformes/Cottoidei | Cottidae | Artediellus fuscimentus | native | Japanese : Nodoguro-okikajika | |
| Perciformes/Cottoidei | Cottidae | Artediellus minor | native | Japanese : Himekajika | |
| Perciformes/Cottoidei | Cottidae | Artediellus neyelovi | native | Japanese : Oshima-okikajika | |
| Perciformes/Cottoidei | Cottidae | Artediellus ochotensis | native | Japanese : Ohotsukukajika | |
| Pleuronectiformes | Soleidae | Aseraggodes cheni | native | ||
| Pleuronectiformes | Soleidae | Aseraggodes kaianus | native | Japanese : Moyô-ushinoshita | |
| Pleuronectiformes | Soleidae | Aseraggodes kobensis | native | Japanese : Tobisasa-ushinoshita | |
| Pleuronectiformes | Soleidae | Aseraggodes orientalis | native | ||
| Pleuronectiformes | Soleidae | Aseraggodes whitakeri | native | Whitaker's sole | |
| Pleuronectiformes | Soleidae | Aseraggodes xenicus | native | Dwarf sole | Japanese : Otome-ushinoshita |
| Perciformes/Zoarcoidei | Opisthocentridae | Askoldia variegata | native | Japanese : Doroginpo | |
| Gobiesociformes | Gobiesocidae | Aspasma minima | native | Japanese : Uba-uo | |
| Gobiesociformes | Gobiesocidae | Aspasmichthys ciconiae | native | Japanese : Tsuru-uba-uo | |
| Blenniiformes | Blenniidae | Aspidontus dussumieri | native | Lance blenny | Japanese : Kurosujiginpo |
| Blenniiformes | Blenniidae | Aspidontus taeniatus | native | False cleanerfish | Japanese : Nise-kurosujiginpo |
| Perciformes/Cottoidei | Agonidae | Aspidophoroides monopterygius | native | Alligatorfish | Japanese : Tatetokubire |
| Ovalentaria/misc | Plesiopidae | Assessor randalli | native | Japanese : Tsubame-tanabata-uo | |
| Scombriformes | Trichiuridae | Assurger anzac | native | Razorback scabbardfish | Japanese : Nagayumetachimodoki |
| Pleuronectiformes | Bothidae | Asterorhombus intermedius | native | Intermediate flounder | Japanese : Seitenbirame |
| Gobiiformes | Gobiidae | Asterropteryx atripes | native | Yano's starry goby | Japanese : Yano uki-hoshihaze |
| Gobiiformes | Gobiidae | Asterropteryx ensifera | native | Miller's damsel | Japanese : Hime-hoshihaze |
| Gobiiformes | Gobiidae | Asterropteryx ovata | native | Oval-spot goby | |
| Gobiiformes | Gobiidae | Asterropteryx semipunctata | native | Starry goby | Japanese : Hoshihaze |
| Gobiiformes | Gobiidae | Asterropteryx senoui | native | Senou's goby | Japanese : Nokogiri-hoshihaze |
| Gobiiformes | Gobiidae | Asterropteryx spinosa | native | Eyebar spiny goby | Japanese : Madara-hoshihaze |
| Gobiiformes | Gobiidae | Astrabe fasciata | native | Japanese : Shima-shirokurahaze | |
| Gobiiformes | Gobiidae | Astrabe flavimaculata | native | Japanese : Kimadarahaze | |
| Gobiiformes | Gobiidae | Astrabe lactisella | native | Japanese : Shirokurahaze | |
| Perciformes/Cottoidei | Cottidae | Astrocottus leprops | endemic | Japanese : Hoho-urokokajika | |
| Perciformes/Cottoidei | Cottidae | Astrocottus matsubarae | native | Japanese : Setokajika | |
| Perciformes/Cottoidei | Cottidae | Astrocottus oyamai | native | Japanese : Ôyamakajika | |
| Perciformes/Cottoidei | Cottidae | Astrocottus regulus | native | ||
| Stomiiformes | Stomiidae | Astronesthes bilobatus | native | Twinlobe snaggletooth | Japanese : Futaba-tokagegisu |
| Stomiiformes | Stomiidae | Astronesthes chrysophekadion | native | Japanese : Gintokagegisu | |
| Stomiiformes | Stomiidae | Astronesthes cyaneus | native | Japanese : Kurotokagegisu | |
| Stomiiformes | Stomiidae | Astronesthes fedorovi | native | ||
| Stomiiformes | Stomiidae | Astronesthes ijimai | native | Ijima's snaggletooth | Japanese : Tokagehadaka |
| Stomiiformes | Stomiidae | Astronesthes indica | native | Black snaggletooth | Japanese : Hohojirotokagegisu |
| Stomiiformes | Stomiidae | Astronesthes indopacificus | native | Indo-Pacific snaggletooth | Japanese : Kuro-tokagegisu |
| Stomiiformes | Stomiidae | Astronesthes lucifer | native | Pacific astronesthid fish | Japanese : Tokagehadaka |
| Stomiiformes | Stomiidae | Astronesthes splendidus | native | Splendid snaggletooth | Japanese : Fusa-kurotokagegisu |
| Stomiiformes | Stomiidae | Astronesthes trifibulatus | native | Triplethread snaggletooth | Japanese : Yari-tokagehadaka |
| Ateleopodiformes | Ateleopodidae | Ateleopus edentatus | native | Japanese : Shiroguchi-shachiburi | |
| Ateleopodiformes | Ateleopodidae | Ateleopus japonicus | native | Pacific jellynose fish | Japanese : Shachiburi |
| Ateleopodiformes | Ateleopodidae | Ateleopus purpureus | native | Japanese : Murasaki-shachiburi | |
| Ateleopodiformes | Ateleopodidae | Ateleopus tanabensis | native | ||
| Carcharhiniformes | Atelomycteridae | Atelomycterus marmoratus | native | Coral catshark | Japanese : Sango-torazame |
| Pleuronectiformes | Pleuronectidae | Atheresthes evermanni | native | Kamchatka flounder | Japanese : Abura garei |
| Atheriniformes | Atherinidae | Atherinomorus lacunosus | native | Hardyhead silverside | Japanese : Yakushima-iwashi |
| Atheriniformes | Atherinidae | Atherinomorus pinguis | native | Narrow-banded hardyhead silverside | Japanese : Hosoobi-yakushima-iwashi |
| Atheriniformes | Atherionidae | Atherion elymus | native | Bearded silverside | Japanese : Mugi-iwashi |
| Perciformes/Cottoidei | Cottidae | Atopocottus tribranchius | native | Japanese : Kawari-anahaze | |
| Eupercaria/misc | Sciaenidae | Atrobucca nibe | native | Blackmouth croaker | Japanese : Kuroguchi |
| Tetraodontiformes | Triacanthodidae | Atrophacanthus japonicus | native | Japanese : Ukeguchikawamuki | |
| Carangiformes | Carangidae | Atropus armatus | native | Longfin trevally | Japanese : Yoroi-aji |
| Carangiformes | Carangidae | Atropus atropos | native | Cleftbelly trevally | Japanese : Kubo-aji |
| Carangiformes | Carangidae | Atropus hedlandensis | native | Bumpnose trevally | Japanese : Ryukyu-yoroi-aji |
| Carangiformes | Carangidae | Atropus mentalis | native | Longrakered trevally | |
| Blenniiformes | Blenniidae | Atrosalarias holomelas | native | Brown coral blenny | Japanese : Indo-kaeru-uo |
| Blenniiformes | Blenniidae | Atrosalarias hosokawai | native | Hosokawa's coral blenny | Japanese : Hosokawa-indo-kaeruuo |
| Carangiformes | Carangidae | Atule mate | native | Yellowtail scad | Japanese : Mate-aji |
| Perciformes/Serranoidei | Liopropomatidae | Aulacocephalus temminckii | native | Goldribbon soapfish | Japanese : Rurihata |
| Perciformes/Gasterosteoidei | Hypoptychidae | Aulichthys japonicus | native | Tubenose | Japanese : Kudayagara |
| Syngnathiformes | Aulostomidae | Aulostomus chinensis | native | Chinese trumpetfish | Japanese : Hera-yagara |
| Trachichthyiformes | Trachichthyidae | Aulotrachichthys prosthemius | native | West Pacific luminous roughy | Japanese : Haridashiebisu |
| Trachichthyiformes | Trachichthyidae | Aulotrachichthys sajademalensis | native | Saya de Malha luminous roughy | Japanese : Minami-haridashiebisu |
| Trachichthyiformes | Trachichthyidae | Aulotrachichthys spiralis | native | Spiralis luminous-roughy | Japanese : Nejitoge-haridashi-ebisu |
| Trachichthyiformes | Trachichthyidae | Aulotrachichthys titan | native | Large-head luminous-roughy | Japanese : Minami-haridashi-ebisu |
| Acanthuriformes | Leiognathidae | Aurigequula fasciata | native | Striped ponyfish | Japanese : Shima-hiiragi |
| Scombriformes | Scombridae | Auxis rochei | native | Bullet tuna | Japanese : Marusôda |
| Scombriformes | Scombridae | Auxis thazard | native | Frigate tuna | Japanese : Soda-gatsuo |
| Anguilliformes | Nemichthyidae | Avocettina infans | native | Avocet snipe eel | Japanese : Kuroshigi-unagi |
| Gobiiformes | Gobiidae | Awaous melanocephalus | native | Largesnout goby | Japanese : Kuro-minamihaze |
| Gobiiformes | Gobiidae | Awaous ocellaris | native | Japanese : Minamihaze | |
| Ovalentaria/misc | Pomacentridae | Azurina elerae | native | Twinspot chromis | Japanese : Taiwan-suzumedai |
| Ovalentaria/misc | Pomacentridae | Azurina lepidolepis | native | Scaly chromis | Japanese : Sasa-suzumedai |
| Alepocephaliformes | Alepocephalidae | Bajacalifornia erimoensis | native | Japanese : Ukeguchi-iwashi | |
| Alepocephaliformes | Alepocephalidae | Bajacalifornia megalops | native | Bigeye smooth-head | |
| Tetraodontiformes | Balistidae | Balistapus undulatus | native | Orange-lined triggerfish | Japanese : Kumadori |
| Tetraodontiformes | Balistidae | Balistoides conspicillum | native | Clown triggerfish | Japanese : Mongarakawahagi |
| Tetraodontiformes | Balistidae | Balistoides viridescens | native | Titan triggerfish | Japanese : Gomamongara |
| Perciformes/Scorpaenoidei | Bembridae | Bambradon laevis | native | ||
| Acropomatiformes | Banjosidae | Banjos banjos | native | Banjofish | Japanese : Chôsenbakama |
| Ophidiiformes | Bythitidae | Barathronus diaphanus | native | ||
| Ophidiiformes | Bythitidae | Barathronus maculatus | native | Spotted gelatinous cusk | |
| Cypriniformes | Nemacheilidae | Barbatula barbatula | native | Stone loach | Japanese : Fukudojô |
| Cypriniformes | Nemacheilidae | Barbatula nuda | native | ||
| Cypriniformes | Nemacheilidae | Barbatula toni | native | ||
| Beryciformes | Barbourisiidae | Barbourisia rufa | native | Velvet whalefish | Japanese : Aka-kujira-uo-damashi |
| Gobiiformes | Gobiidae | Barbuligobius boehlkei | native | Cryptic bearded goby | Japanese : Higemojahaze |
| Anguilliformes | Ophichthidae | Bascanichthys ryukyuensis | native | Vine-like sand eel | Japanese : Kazura-umihebi |
| Ophidiiformes | Ophidiidae | Bassozetus levistomatus | native | ||
| Ophidiiformes | Ophidiidae | Bassozetus zenkevitchi | native | Japanese : Fukumen-itachiuo | |
| Stomiiformes | Stomiidae | Bathophilus brevis | native | Japanese : Maru-ginga-eso | |
| Stomiiformes | Stomiidae | Bathophilus digitatus | native | Japanese : Chihiro-hoshi-eso | |
| Stomiiformes | Stomiidae | Bathophilus nigerrimus | native | Scaleless dragonfish | Japanese : Ginga-eso |
| Stomiiformes | Stomiidae | Bathophilus pawneei | native | Pawnee dragonfish | Japanese : Hoso-ginga-eso |
| Callionymiformes | Callionymidae | Bathycallionymus kaianus | native | Kai Island deepwater dragonet | Japanese : Tongari-numeri |
| Acropomatiformes | Bathyclupeidae | Bathyclupea nikparini | native | Deepsea herring | |
| Anguilliformes | Congridae | Bathycongrus retrotinctus | native | Blackedge conger | Japanese : Tsumaguro-anago |
| Anguilliformes | Congridae | Bathycongrus wallacei | native | Longnose conger | |
| Gadiformes | Bathygadidae | Bathygadus antrodes | native | Japanese : Anadara | |
| Gadiformes | Bathygadidae | Bathygadus garretti | native | Japanese : Hige-anadara | |
| Gadiformes | Bathygadidae | Bathygadus nipponicus | native | Japanese : Tsukaidara | |
| Gobiiformes | Gobiidae | Bathygobius coalitus | native | Whitespotted frillgoby | Japanese : Kuro-yahazuhaze |
| Gobiiformes | Gobiidae | Bathygobius cocosensis | native | Cocos frill-goby | Japanese : Sujikumohaze |
| Gobiiformes | Gobiidae | Bathygobius cotticeps | native | Cheekscaled frill-goby | Japanese : Kusabihaze |
| Gobiiformes | Gobiidae | Bathygobius cyclopterus | native | Spotted frillgoby | Japanese : Yahazuhaze |
| Gobiiformes | Gobiidae | Bathygobius fuscus | native | Dusky frillgoby | Japanese : Kumohaze |
| Gobiiformes | Gobiidae | Bathygobius hongkongensis | native | Japanese : Kurohoshi-yahazuhaze | |
| Gobiiformes | Gobiidae | Bathygobius meggitti | native | Meggitt's goby | |
| Gobiiformes | Gobiidae | Bathygobius petrophilus | native | Japanese : Shijimihaze | |
| Argentiniformes | Bathylagidae | Bathylagus pacificus | native | Slender blacksmelt | Japanese : Yase-soko-iwashi |
| Argentiniformes | Opisthoproctidae | Bathylychnops exilis | native | Javelin spookfish | Japanese : Mukashi-demenigisu |
| Perciformes/Zoarcoidei | Bathymasteridae | Bathymaster derjugini | native | Japanese : Sumitsuki-medamauo | |
| Perciformes/Zoarcoidei | Bathymasteridae | Bathymaster leurolepis | native | Smallmouth ronquil | Japanese : Madara-medamauo |
| Perciformes/Zoarcoidei | Bathymasteridae | Bathymaster signatus | native | Searcher | Japanese : Soko-medamauo |
| Ophidiiformes | Ophidiidae | Bathyonus caudalis | native | ||
| Tetraodontiformes | Triacanthodidae | Bathyphylax omen | native | Japanese : Yami-kawamuki | |
| Aulopiformes | Ipnopidae | Bathypterois atricolor | native | Attenuated spider fish | Japanese : Itohiki-iwashi |
| Aulopiformes | Ipnopidae | Bathypterois guentheri | native | Tribute spiderfish | Japanese : Nagazue-eso |
| Rajiformes | Arhynchobatidae | Bathyraja abyssicola | native | Deep-sea skate | Japanese : Chihirokasube |
| Rajiformes | Arhynchobatidae | Bathyraja aleutica | native | Aleutian skate | Japanese : Arasukakasube |
| Rajiformes | Arhynchobatidae | Bathyraja andriashevi | native | Little-eyed skate | |
| Rajiformes | Arhynchobatidae | Bathyraja bergi | native | Bottom skate | |
| Rajiformes | Arhynchobatidae | Bathyraja caeluronigricans | native | Purple-black skate | Japanese : Tsumurakasube |
| Rajiformes | Arhynchobatidae | Bathyraja diplotaenia | native | Dusky-pink skate | Japanese : Ribonkasube |
| Rajiformes | Arhynchobatidae | Bathyraja fedorovi | native | Cinnamon skate | |
| Rajiformes | Arhynchobatidae | Bathyraja isotrachys | native | Raspback skate | Japanese : Charenja-kasube |
| Rajiformes | Arhynchobatidae | Bathyraja lindbergi | native | Commander skate | Japanese : Komandorukasube |
| Rajiformes | Arhynchobatidae | Bathyraja maculata | native | White-blotched skate | |
| Rajiformes | Arhynchobatidae | Bathyraja matsubarai | native | Dusky-purple skate | Japanese : Matsubara-ei |
| Rajiformes | Arhynchobatidae | Bathyraja minispinosa | native | Whitebrow skate | Japanese : Subesubekasube |
| Rajiformes | Arhynchobatidae | Bathyraja notoroensis | native | Notoro skate | Japanese : Notorokasube |
| Rajiformes | Arhynchobatidae | Bathyraja pseudoisotrachys | native | Japanese : Soko-gangiei | |
| Rajiformes | Arhynchobatidae | Bathyraja smirnovi | native | Golden skate | Japanese : Dobukasube |
| Rajiformes | Arhynchobatidae | Bathyraja trachouros | native | Eremo skate | Japanese : Zarakasube |
| Rajiformes | Arhynchobatidae | Bathyraja violacea | native | Okhotsk skate | Japanese : Kitanokasube |
| Aulopiformes | Bathysauroididae | Bathysauroides gigas | native | Pale deepsea lizardfish | Japanese : Oni-aome-eso |
| Aulopiformes | Bathysauridae | Bathysaurus mollis | native | Highfin lizardfish | Japanese : Shinkai-eso |
| Acropomatiformes | Howellidae | Bathysphyraenops simplex | native | Japanese : Toge-sumikui-uo | |
| Myliobatiformes | Dasyatidae | Bathytoshia brevicaudata | native | Short-tail stingray | Japanese : Hoshi-ei; Japanese : Ushi-ei; |
| Myliobatiformes | Dasyatidae | Bathytoshia lata | native | Brown stingray | |
| Anguilliformes | Congridae | Bathyuroconger parvibranchialis | native | Small-gill large-toothed conger | |
| Anguilliformes | Congridae | Bathyuroconger vicinus | native | Large-toothed conger | Japanese : Soko-ai-anago |
| Gobiiformes | Eleotridae | Belobranchus belobranchus | native | Throat-spine gudgeon | |
| Ovalentaria/misc | Plesiopidae | Belonepterygion fasciolatum | native | Barred spiny basslet | Japanese : Togetanabata-uo |
| Perciformes/Serranoidei | Liopropomatidae | Belonoperca chabanaudi | native | Arrowhead soapfish | Japanese : Yamisuzuki |
| Perciformes/Scorpaenoidei | Bembridae | Bembradium roseum | native | Japanese : Barahaigochi | |
| Perciformes/Scorpaenoidei | Bembridae | Bembras japonica | native | Japanese : Akagochi | |
| Perciformes/Bembropoidei | Bembropidae | Bembrops caudimacula | native | Japanese : Aitoragisu | |
| Perciformes/Bembropoidei | Bembropidae | Bembrops curvatura | native | Japanese : Nami-aitoragisu | |
| Perciformes/Bembropoidei | Bembropidae | Bembrops filiferus | native | Sharpnosed duckbill | Japanese : Itohiki-aitoragisu |
| Aulopiformes | Scopelarchidae | Benthalbella dentata | native | Northern pearleye | Japanese : Tsumari-deme-eso |
| Aulopiformes | Scopelarchidae | Benthalbella infans | native | Zugmayer's pearleye | Japanese : Hikari-deme-eso |
| Aulopiformes | Scopelarchidae | Benthalbella linguidens | native | Longfin pearleye | Japanese : Deme-eso |
| Scombriformes | Trichiuridae | Benthodesmus pacificus | native | North-Pacific frostfish | Japanese : Hoso-tachimodoki |
| Scombriformes | Trichiuridae | Benthodesmus tenuis | native | Slender frostfish | Japanese : Tachimodoki |
| Scombriformes | Trichiuridae | Benthodesmus vityazi | native | Vityaz' frostfish | |
| Myctophiformes | Myctophidae | Benthosema fibulatum | native | Spinycheek lanternfish | Japanese : Hokuto-hadaka |
| Myctophiformes | Myctophidae | Benthosema pterotum | native | Skinnycheek lanternfish | Japanese : Iwa-hadaka |
| Myctophiformes | Myctophidae | Benthosema suborbitale | native | Smallfin lanternfish | Japanese : Soko-hadaka |
| Rajiformes | Rajidae | Beringraja pulchra | native | Mottled skate | Japanese : Meganekasube |
| Perciformes/Cottoidei | Cottidae | Bero elegans | native | Japanese : Bero | |
| Lophiiformes | Oneirodidae | Bertella idiomorpha | native | Japanese : Bâterusen-ankô | |
| Beryciformes | Berycidae | Beryx decadactylus | native | Alfonsino | Japanese : Nanyôkinme |
| Beryciformes | Berycidae | Beryx mollis | native | Japanese : Fūsen-kinme | |
| Beryciformes | Berycidae | Beryx splendens | native | Splendid alfonsino | Japanese : Kinmedai |
| Perciformes/Zoarcoidei | Zoarcidae | Bilabria gigantea | native | Japanese : Hirokuchi-genge | |
| Perciformes/Zoarcoidei | Zoarcidae | Bilabria ornata | native | Japanese : Mitsukuchigenge | |
| Cypriniformes | Gobionidae | Biwia tama | native | ||
| Cypriniformes | Gobionidae | Biwia yodoensis | native | Japanese : Yodo-zezera | |
| Cypriniformes | Gobionidae | Biwia zezera | native | Japanese : Zezera | |
| Perciformes/Uranoscopoidei | Ammodytidae | Bleekeria mitsukurii | native | Mitsukuri's sandlance | Japanese : Taiwan-ikanago |
| Blenniiformes | Blenniidae | Blenniella bilitonensis | native | Biliton blenniella | Japanese : Hohoguroginpo |
| Blenniiformes | Blenniidae | Blenniella caudolineata | native | Blue-spotted blenny | Japanese : Aotenginpo |
| Blenniiformes | Blenniidae | Blenniella chrysospilos | native | Red-spotted blenny | Japanese : Montsuki-kaeru-uo |
| Blenniiformes | Blenniidae | Blenniella gibbifrons | native | Hump-headed blenny | |
| Blenniiformes | Blenniidae | Blenniella paula | native | Bluedash rockskipper | |
| Blenniiformes | Blenniidae | Blenniella periophthalmus | native | Blue-dashed rockskipper | Japanese : Hana kaeru uo |
| Perciformes/Cottoidei | Agonidae | Blepsias bilobus | native | Crested sculpin | Japanese : Hokake-anahaze |
| Perciformes/Cottoidei | Agonidae | Blepsias cirrhosus | native | Silverspotted sculpin | Japanese : Isobatengu |
| Eupercaria/misc | Labridae | Bodianus anthioides | native | Lyretail hogfish | Japanese : Hiodoshibera |
| Eupercaria/misc | Labridae | Bodianus axillaris | native | Axilspot hogfish | Japanese : Sumitsukibera |
| Eupercaria/misc | Labridae | Bodianus bilunulatus | native | Tarry hogfish | Japanese : Kitsunebera |
| Eupercaria/misc | Labridae | Bodianus bimaculatus | native | Twospot hogfish | Japanese : Futahoshi-kitsunebera |
| Eupercaria/misc | Labridae | Bodianus cylindriatus | native | Japanese : Akabô | |
| Eupercaria/misc | Labridae | Bodianus dictynna | native | Redfin hogfish | |
| Eupercaria/misc | Labridae | Bodianus izuensis | native | Striped pigfish | Japanese : Tanukibera |
| Eupercaria/misc | Labridae | Bodianus leucosticticus | native | Lined hogfish | |
| Eupercaria/misc | Labridae | Bodianus loxozonus | native | Blackfin hogfish | Japanese : Blackfin hogfish |
| Eupercaria/misc | Labridae | Bodianus masudai | native | Japanese : Shima-kitsunebera | |
| Eupercaria/misc | Labridae | Bodianus mesothorax | native | Splitlevel hogfish | Japanese : Kesagakebera |
| Eupercaria/misc | Labridae | Bodianus oxycephalus | native | Japanese : Kitsunedai | |
| Eupercaria/misc | Labridae | Bodianus perditio | native | Golden-spot hogfish | Japanese : Takibera |
| Eupercaria/misc | Labridae | Bodianus reticulatus | native | Japanese : Kobudai | |
| Eupercaria/misc | Labridae | Bodianus tanyokidus | native | Japanese : Zunaga-akabô | |
| Eupercaria/misc | Labridae | Bodianus thoracotaeniatus | native | Japanese : Itohiki-akabô | |
| Eupercaria/misc | Scaridae | Bolbometopon muricatum | native | Green humphead parrotfish | Japanese : Kanmuribudai |
| Gobiiformes | Oxudercidae | Boleophthalmus pectinirostris | native | Great blue spotted mudskipper | Japanese : Mutsugorô |
| Myctophiformes | Myctophidae | Bolinichthys distofax | native | Japanese : Futo-mikazuki-hadaka | |
| Myctophiformes | Myctophidae | Bolinichthys longipes | native | Popeye lampfish | Japanese : Hoso-mikazuki-hadaka |
| Myctophiformes | Myctophidae | Bolinichthys pyrsobolus | native | Fiery lanternfish | |
| Myctophiformes | Myctophidae | Bolinichthys supralateralis | native | Stubby lanternfish | Japanese : Mikazuki-hadaka |
| Stomiiformes | Stomiidae | Borostomias elucens | native | Japanese : Sukibatokagegisu | |
| Stomiiformes | Stomiidae | Borostomias pacificus | native | Japanese : Futasuboshi-hoshi-eso | |
| Gobiiformes | Butidae | Bostrychus sinensis | native | Four-eyed sleeper | Japanese : Janome-haze |
| Perciformes/Cottoidei | Agonidae | Bothragonus occidentalis | native | Japanese : Saitokubire | |
| Perciformes/Zoarcoidei | Zoarcidae | Bothrocara hollandi | native | Japanese : Norogenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Bothrocara molle | native | Soft eelpout | Japanese : Shirogenge |
| Perciformes/Zoarcoidei | Zoarcidae | Bothrocara tanakae | native | Japanese : Kantengenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Bothrocarina microcephala | native | Japanese : Kamuchakkagenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Bothrocarina nigrocaudata | native | Japanese : Ogurogenge | |
| Pleuronectiformes | Bothidae | Bothus mancus | native | Flowery flounder | Japanese : Mondarumagarei |
| Pleuronectiformes | Bothidae | Bothus myriaster | native | Indo-Pacific oval flounder | Japanese : Hoshidarumagarei |
| Pleuronectiformes | Bothidae | Bothus pantherinus | native | Leopard flounder | Japanese : Togedarumagarei |
| Tetraodontiformes | Monacanthidae | Brachaluteres ulvarum | native | Japanese inflator filefish | Japanese : Aosahagi |
| Pleuronectiformes | Soleidae | Brachirus annularis | native | Annular sole | Japanese : Wamon-ushinoshita |
| Pleuronectiformes | Soleidae | Brachirus aspilos | native | Japanese : Amami-ushinoshita | |
| Pleuronectiformes | Soleidae | Brachirus orientalis | native | Oriental sole | Japanese : Minamishima-ushinoshita |
| Perciformes/Cottoidei | Agonidae | Brachyopsis segaliensis | native | Japanese : Shichirô-uo | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Brachypterois serrulata | native | Sawcheek scorpionfish | Japanese : Nokogirikasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Brachypterois serrulifer | native | Sawmaxilla scorpionfish | |
| Anguilliformes | Ophichthidae | Brachysomophis cirrocheilos | native | Stargazer snake eel | Japanese : Moyô-tatsu-umihebi |
| Anguilliformes | Ophichthidae | Brachysomophis crocodilinus | native | Crocodile snake eel | Japanese : Tatsu-umihebi |
| Anguilliformes | Ophichthidae | Brachysomophis henshawi | native | Reptilian snake eel | |
| Anguilliformes | Ophichthidae | Brachysomophis porphyreus | native | Japanese : Murasaki-umihebi | |
| Scombriformes | Bramidae | Brama dussumieri | native | Lesser bream | Japanese : Hirenaga-shimagatsuo |
| Scombriformes | Bramidae | Brama japonica | native | Pacific pomfret | Japanese : Shimagatsuo |
| Scombriformes | Bramidae | Brama myersi | native | Myers' pomfret | Japanese : Onaga-shimagatsuo |
| Scombriformes | Bramidae | Brama orcini | native | Bigtooth pomfret | Japanese : Shimagatsuo-zoku-no-isshu |
| Eupercaria/misc | Latilidae | Branchiostegus albus | native | Japanese : Shiro-amadai | |
| Eupercaria/misc | Latilidae | Branchiostegus argentatus | native | Japanese : Sumitsuki-amadai | |
| Eupercaria/misc | Latilidae | Branchiostegus auratus | native | Japanese : Ki-amadai | |
| Eupercaria/misc | Latilidae | Branchiostegus japonicus | native | Horsehead tilefish | Japanese : Aka-amadai |
| Gadiformes | Bregmacerotidae | Bregmaceros anchovia | native | False anchovy codlet | Japanese : Hitosuji-saiuo |
| Gadiformes | Bregmacerotidae | Bregmaceros japonicus | native | Japanese codlet | Japanese : Saiuo |
| Gadiformes | Bregmacerotidae | Bregmaceros nectabanus | native | Smallscale codlet | Japanese : Toyama-saiuo |
| Gadiformes | Bregmacerotidae | Bregmaceros neonectabanus | native | Japanese : Kurohara-saiuo | |
| Gadiformes | Bregmacerotidae | Bregmaceros retrodorsalis | native | Back-fin codlet | Japanese : Gomafu-saiuo |
| Ophidiiformes | Bythitidae | Brosmophyciops pautzkei | native | Slimy cuskeel | Japanese : Chibi-numeri-itachiuo |
| Ophidiiformes | Ophidiidae | Brotula multibarbata | native | Goatsbeard brotula | Japanese : Itachiuo |
| Ophidiiformes | Ophidiidae | Brotulotaenia nielseni | native | ||
| Gobiiformes | Gobiidae | Bryaninops amplus | native | Large whip goby | |
| Gobiiformes | Gobiidae | Bryaninops isis | native | Isis goby | Japanese : Kobito-garasuhaze |
| Gobiiformes | Gobiidae | Bryaninops loki | native | Loki whip-goby | |
| Gobiiformes | Gobiidae | Bryaninops natans | native | Redeye goby | |
| Gobiiformes | Gobiidae | Bryaninops ridens | native | Ridens goby | Japanese : Somewakehaze |
| Gobiiformes | Gobiidae | Bryaninops yongei | native | Whip coral goby | Japanese : Garasuhaze |
| Perciformes/Zoarcoidei | Stichaeidae | Bryozoichthys lysimus | native | Nutcracker prickleback | Japanese : Fusakakeginpo |
| Gobiiformes | Butidae | Butis amboinensis | native | Olive flathead-gudgeon | Japanese : Yaeyamanokogirihaze |
| Gobiiformes | Gobiidae | Cabillus atripelvicus | endemic | ||
| Gobiiformes | Gobiidae | Cabillus lacertops | native | Lizard cabillus | Japanese : Mikagehaze |
| Gobiiformes | Gobiidae | Cabillus pexus | endemic | Japanese : Kushi-yorime-haze | |
| Gobiiformes | Gobiidae | Cabillus tongarevae | native | Tongareva goby | Japanese : Yorimehaze |
| Anguilliformes | Ophichthidae | Caecula kuro | native | Japanese : Kuro-umihebi | |
| Eupercaria/misc | Caesionidae | Caesio caerulaurea | native | Blue and gold fusilier | Japanese : Sasamuro |
| Eupercaria/misc | Caesionidae | Caesio cuning | native | Redbelly yellowtail fusilier | Japanese : Yumeumeiro |
| Eupercaria/misc | Caesionidae | Caesio lunaris | native | Lunar fusilier | Japanese : Hana-takasago |
| Eupercaria/misc | Caesionidae | Caesio teres | native | Yellow and blueback fusilier | |
| Eupercaria/misc | Callanthiidae | Callanthias japonicus | native | Japanese : Shikishimahanadai | |
| Anguilliformes | Ophichthidae | Callechelys catostoma | native | Black-striped snake eel | Japanese : Himo-umihebi |
| Callionymiformes | Callionymidae | Callionymus beniteguri | native | Whitespotted dragonet | Japanese : Tobi-numeri |
| Callionymiformes | Callionymidae | Callionymus curvicornis | native | Horn dragonet | Japanese : Nezumi-gochi |
| Callionymiformes | Callionymidae | Callionymus curvispinis | endemic | Izu ruddertail dragonet | Japanese : Chibi-numeri |
| Callionymiformes | Callionymidae | Callionymus doryssus | native | Japanese filamentous dragonet | Japanese : Yari-numeri |
| Callionymiformes | Callionymidae | Callionymus draconis | native | Japanese spiny dragonet | Japanese : Japanese spiny dragonet; Japanese : Tatsu-numeri; |
| Callionymiformes | Callionymidae | Callionymus enneactis | native | Mangrove dragonet | Japanese : Hanabi-numeri; Japanese : Kogata-hanabi-numeri; |
| Callionymiformes | Callionymidae | Callionymus formosanus | native | Taiwanese deepwater dragonet | Japanese : Kujaku-soko-numeri |
| Callionymiformes | Callionymidae | Callionymus ikedai | native | Ryukyu ruddertail dragonet | Japanese : Narita-itohiki-numeri |
| Callionymiformes | Callionymidae | Callionymus izuensis | native | Izu dragonet | Japanese : Izu-numeri |
| Callionymiformes | Callionymidae | Callionymus japonicus | native | Japanese longtail dragonet | Japanese : Yome-gochi |
| Callionymiformes | Callionymidae | Callionymus lunatus | native | Moon dragonet | Japanese : Numerigochi |
| Callionymiformes | Callionymidae | Callionymus ochiaii | native | Japanese lowfin deepwater dragonet | English : Japanese lowfin deepwater dragonet |
| Callionymiformes | Callionymidae | Callionymus planus | native | Japanese darter dragonet | Japanese : Hera-numeri |
| Callionymiformes | Callionymidae | Callionymus pleurostictus | native | Blue-spotted ruddertail dragonet | Japanese : Chishima-tokubire |
| Callionymiformes | Callionymidae | Callionymus sokonumeri | native | Japanese highfin deepwater dragonet | Japanese : Soko-numeri |
| Callionymiformes | Callionymidae | Callionymus valenciennei | native | Valenciennes' dragonet | Japanese : Hatatate-numeri |
| Gobiiformes | Gobiidae | Callogobius albipunctatus | native | Japanese : Awayuki-futasuji-haze | |
| Gobiiformes | Gobiidae | Callogobius dorsomaculatus | native | Japanese : Seboshi-futasuji-haze | |
| Gobiiformes | Gobiidae | Callogobius falx | native | Wagtail Goby | Japanese : Sekirei-haze |
| Gobiiformes | Gobiidae | Callogobius hasseltii | native | Hasselt's goby | Japanese : Okinawahaze |
| Gobiiformes | Gobiidae | Callogobius hastatus | native | Spearfin goby | |
| Gobiiformes | Gobiidae | Callogobius maculipinnis | native | Ostrich goby | |
| Gobiiformes | Gobiidae | Callogobius okinawae | native | Okinawa flap-headed goby | Japanese : Namerahaze |
| Gobiiformes | Gobiidae | Callogobius sclateri | native | Pacific goby | Japanese : Futasujihaze |
| Gobiiformes | Gobiidae | Callogobius shunkan | native | ||
| Gobiiformes | Gobiidae | Callogobius snelliusi | native | Japanese : Shunkanhaze | |
| Gobiiformes | Gobiidae | Callogobius tanegasimae | native | Japanese : Tanehaze | |
| Ovalentaria/misc | Plesiopidae | Calloplesiops altivelis | native | Comet | Japanese : Shimofuri-tanabata-uo |
| Eupercaria/misc | Scaridae | Calotomus carolinus | native | Carolines parrotfish | |
| Eupercaria/misc | Scaridae | Calotomus japonicus | native | Japanese parrotfish | Japanese : Budai |
| Eupercaria/misc | Scaridae | Calotomus spinidens | native | Spinytooth parrotfish | Japanese : Taiwan-budai |
| Tetraodontiformes | Monacanthidae | Cantherhines dumerilii | native | Whitespotted filefish | Japanese : Hakuseihagi |
| Tetraodontiformes | Monacanthidae | Cantherhines fronticinctus | native | Spectacled filefish | Japanese : Megane-umazurahagi |
| Tetraodontiformes | Monacanthidae | Cantherhines pardalis | native | Honeycomb filefish | Japanese : Amime-umazurahagi |
| Tetraodontiformes | Balistidae | Canthidermis macrolepis | native | Largescale triggerfish | |
| Tetraodontiformes | Balistidae | Canthidermis maculata | native | Rough triggerfish | Japanese : Amimongara |
| Tetraodontiformes | Balistidae | Canthidermis rotundatus | native | ||
| Tetraodontiformes | Tetraodontidae | Canthigaster amboinensis | native | Spider-eye puffer | |
| Tetraodontiformes | Tetraodontidae | Canthigaster axiologus | native | Pacific crown toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster bennetti | native | Bennett's sharpnose puffer | Japanese : Kazarikinchakufugu |
| Tetraodontiformes | Tetraodontidae | Canthigaster compressa | native | Compressed toby | Japanese : Himekinchakufugu |
| Tetraodontiformes | Tetraodontidae | Canthigaster epilampra | native | Lantern toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster inframacula | native | Japanese : Hokuro-kinchakufugu | |
| Tetraodontiformes | Tetraodontidae | Canthigaster janthinoptera | native | Honeycomb toby | Japanese : Gomafukinchakufugu |
| Tetraodontiformes | Tetraodontidae | Canthigaster ocellicincta | native | Shy toby | |
| Tetraodontiformes | Tetraodontidae | Canthigaster rivulata | native | Brown-lined puffer | Japanese : Kitamakura |
| Tetraodontiformes | Tetraodontidae | Canthigaster solandri | native | Spotted sharpnose | |
| Tetraodontiformes | Tetraodontidae | Canthigaster valentini | native | Valentin's sharpnose puffer | Japanese : Shima-kinchakufugu |
| Perciformes/Serranoidei | Anthiadidae | Caprodon affinis | native | ||
| Perciformes/Serranoidei | Anthiadidae | Caprodon schlegelii | native | Sunrise perch | Japanese : Akaisaki |
| Perciformes/Scorpaenoidei | Scorpaenidae | Caracanthus maculatus | native | Spotted coral croucher | Japanese : Dango-okoze |
| Perciformes/Scorpaenoidei | Scorpaenidae | Caracanthus unipinna | native | Pygmy coral croucher | Japanese : Watage-dango-okoze |
| Gobiiformes | Gobiidae | Caragobius urolepis | native | Scaleless worm goby | Japanese : Asagarahaze |
| Carangiformes | Carangidae | Carangichthys dinema | native | Shadow trevally | Japanese : Itohira-aji |
| Carangiformes | Carangidae | Carangichthys oblongus | native | Coachwhip trevally | Japanese : Tenjiku-aji |
| Carangiformes | Carangidae | Caranx heberi | native | Blacktip trevally | |
| Carangiformes | Carangidae | Caranx ignobilis | native | Giant trevally | Japanese : Rônin-aji |
| Carangiformes | Carangidae | Caranx lugubris | native | Black jack | Japanese : Kappore |
| Carangiformes | Carangidae | Caranx melampygus | native | Bluefin trevally | Japanese : Kasumi-aji |
| Carangiformes | Carangidae | Caranx papuensis | native | Brassy trevally | Japanese : Onihara-aji |
| Carangiformes | Carangidae | Caranx sexfasciatus | native | Bigeye trevally | Japanese : Gingame-aji |
| Carangiformes | Carangidae | Caranx tille | native | Tille trevally | Japanese : Minami-gingame aji |
| Ophidiiformes | Carapidae | Carapus mourlani | native | Star pearlfish | Japanese : Kazari-kakureuo |
| Cypriniformes | Cyprinidae | Carassius auratus | native | Goldfish | Japanese : Kin-buna; Japanese : Naga-buna; Japanese : Nigoro-buna; |
| Cypriniformes | Cyprinidae | Carassius carassius | native | Crucian carp | Japanese : Funa |
| Cypriniformes | Cyprinidae | Carassius cuvieri | native | Japanese white crucian carp | Japanese : Gengorô-buna |
| Cypriniformes | Cyprinidae | Carassius langsdorfii | native | Japanese : Gin-buna | |
| Carcharhiniformes | Carcharhinidae | Carcharhinus albimarginatus | native | Silvertip shark | Japanese : Tsumajiro |
| Carcharhiniformes | Carcharhinidae | Carcharhinus brachyurus | native | Copper shark | Japanese : Kuroherimejiro |
| Carcharhiniformes | Carcharhinidae | Carcharhinus brevipinna | native | Spinner shark | Japanese : Hanazame |
| Carcharhiniformes | Carcharhinidae | Carcharhinus falciformis | native | Silky shark | Japanese : Kurotogarizame |
| Carcharhiniformes | Carcharhinidae | Carcharhinus galapagensis | native | Galapagos shark | Japanese : Garapagosu zame |
| Carcharhiniformes | Carcharhinidae | Carcharhinus limbatus | native | Blacktip shark | Japanese : Kamasutogari zame |
| Carcharhiniformes | Carcharhinidae | Carcharhinus macloti | native | Hardnose shark | Japanese : Hokosaki |
| Carcharhiniformes | Carcharhinidae | Carcharhinus melanopterus | native | Blacktip reef shark | Japanese : Tsumaguro |
| Carcharhiniformes | Carcharhinidae | Carcharhinus obscurus | native | Dusky shark | Japanese : Dotabuka |
| Carcharhiniformes | Carcharhinidae | Carcharhinus plumbeus | native | Sandbar shark | Japanese : Mejirozame |
| Carcharhiniformes | Carcharhinidae | Carcharhinus sorrah | native | Spot-tail shark | Japanese : Houraizame |
| Lamniformes | Carchariidae | Carcharias taurus | native | Sand tiger shark | Japanese : Shirowani |
| Lamniformes | Lamnidae | Carcharodon carcharias | native | Great white shark | Japanese : Hohojirozame |
| Perciformes/Cottoidei | Liparidae | Careproctus acanthodes | native | Japanese : Toge-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus ambustus | native | Scorched snailfish | |
| Perciformes/Cottoidei | Liparidae | Careproctus barbatulus | native | Japanese : Isaribi-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus colletti | native | Alaska snailfish | Japanese : Arasuka-bikunin |
| Perciformes/Cottoidei | Liparidae | Careproctus cyclocephalus | native | Japanese : Daruma-konnyaku-uo | |
| Perciformes/Cottoidei | Liparidae | Careproctus cypselurus | native | Falcate snailfish | Japanese : Ai-bikunin |
| Perciformes/Cottoidei | Liparidae | Careproctus furcellus | native | Japanese : Oguro-konnyaku-uo | |
| Perciformes/Cottoidei | Liparidae | Careproctus io | native | Japanese : Mini-kon’nyakuuo | |
| Perciformes/Cottoidei | Liparidae | Careproctus longibarbatus | native | Japanese : Hige-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus marginatus | native | Japanese : Hireguro-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus mederi | native | ||
| Perciformes/Cottoidei | Liparidae | Careproctus notosaikaiensis | native | Notosaikai-bikunin | Japanese : Notosaikai-bikunin |
| Perciformes/Cottoidei | Liparidae | Careproctus parvidiscus | native | Japanese : Shiretoko-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus rastrinus | native | Salmon snailfish | Japanese : Ao-bikunin |
| Perciformes/Cottoidei | Liparidae | Careproctus rhodomelas | native | Japanese : Bara-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus rotundifrons | native | Japanese : Hime-kon'nyakuuo | |
| Perciformes/Cottoidei | Liparidae | Careproctus simus | native | Japanese : Tengu-konnyaku-uo | |
| Perciformes/Cottoidei | Liparidae | Careproctus sinensis | native | Japanese : Sekichiku-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus spinulosus | native | Japanese : Tomoshibi-bikunin | |
| Perciformes/Cottoidei | Liparidae | Careproctus surugaensis | native | Suruga snailfsh | Japanese : Suruga-bikunin |
| Perciformes/Cottoidei | Liparidae | Careproctus trachysoma | native | Japanese : Zara-bikunin | |
| Scombriformes | Caristiidae | Caristius macropus | native | Manefish | Japanese : Yaegisu |
| Ophidiiformes | Bythitidae | Cataetyx lepidogenys | native | Japanese : Fusa itachiuo | |
| Ophidiiformes | Bythitidae | Cataetyx platyrhynchus | native | Japanese : Ô-soko-itachiuo | |
| Lophiiformes | Caulophrynidae | Caulophryne jordani | native | Fanfin angler | Japanese : Hirenagachôchin-ankô |
| Lophiiformes | Caulophrynidae | Caulophryne pelagica | native | ||
| Syngnathiformes | Centriscidae | Centriscus scutatus | native | Grooved razor-fish | Japanese : Yoroi-uo |
| Beryciformes | Berycidae | Centroberyx druzhinini | native | Japanese : Kinmedamashi | |
| Beryciformes | Berycidae | Centroberyx lineatus | native | Swallow-tail | |
| Myctophiformes | Myctophidae | Centrobranchus andreae | native | Andre's lanternfish | Japanese : Maruhana-hadaka |
| Myctophiformes | Myctophidae | Centrobranchus brevirostris | native | Japanese : Buta-hadaka | |
| Myctophiformes | Myctophidae | Centrobranchus choerocephalus | native | Japanese : Nagahana-hadaka | |
| Callionymiformes | Draconettidae | Centrodraco nakaboi | native | Nakabo's slope dragonet | |
| Callionymiformes | Draconettidae | Centrodraco otohime | native | Japanese : Otohime-numeri | |
| Callionymiformes | Draconettidae | Centrodraco pseudoxenicus | native | Japanese slope dragonet | Japanese : Hanagasa-numeri |
| Eupercaria/misc | Centrogenyidae | Centrogenys vaigiensis | native | False scorpionfish | Japanese : Onihata |
| Squaliformes | Centrophoridae | Centrophorus atromarginatus | native | Dwarf gulper shark | |
| Squaliformes | Centrophoridae | Centrophorus granulosus | native | Gulper shark | Japanese : Tarôzame; Japanese : Uroko-aizame; |
| Squaliformes | Centrophoridae | Centrophorus moluccensis | native | Smallfin gulper shark | Japanese : Okinawa-yajirizame |
| Squaliformes | Centrophoridae | Centrophorus squamosus | native | Leafscale gulper shark | Japanese : Momijizame |
| Squaliformes | Centrophoridae | Centrophorus tessellatus | native | Mosaic gulper shark | Japanese : Genrokuzame |
| Squaliformes | Centrophoridae | Centrophorus uyato | native | Little gulper shark | |
| Lophiiformes | Centrophrynidae | Centrophryne spinulosa | native | Horned lantern fish | |
| Acanthuriformes | Pomacanthidae | Centropyge bicolor | native | Bicolor angelfish | Japanese : Somewakeyakko |
| Acanthuriformes | Pomacanthidae | Centropyge bispinosa | native | Twospined angelfish | Japanese : Ruriyakko |
| Acanthuriformes | Pomacanthidae | Centropyge ferrugata | native | Rusty angelfish | Japanese : Akaharayakko |
| Acanthuriformes | Pomacanthidae | Centropyge fisheri | native | Orange angelfish | Japanese : Chairoyakko |
| Acanthuriformes | Pomacanthidae | Centropyge flavissima | native | Lemonpeel angelfish | Japanese : Koganeyakko |
| Acanthuriformes | Pomacanthidae | Centropyge heraldi | native | Yellow angelfish | Japanese : Herarudo-koganeyakko |
| Acanthuriformes | Pomacanthidae | Centropyge interrupta | native | Japanese angelfish | Japanese : Retenyakko |
| Acanthuriformes | Pomacanthidae | Centropyge nox | native | Midnight angelfish | Japanese : Ohaguroyakko |
| Acanthuriformes | Pomacanthidae | Centropyge shepardi | native | Mango angelfish | Japanese : Daidaiyakko |
| Acanthuriformes | Pomacanthidae | Centropyge tibicen | native | Keyhole angelfish | Japanese : Aburayakko |
| Acanthuriformes | Pomacanthidae | Centropyge venusta | native | Purplemask angelfish | Japanese : Sumireyakko |
| Acanthuriformes | Pomacanthidae | Centropyge vrolikii | native | Pearlscale angelfish | Japanese : Namerayakko |
| Squaliformes | Etmopteridae | Centroscyllium kamoharai | native | Bareskin dogfish | Japanese : Hadaka-kasumizame |
| Squaliformes | Etmopteridae | Centroscyllium ritteri | endemic | Whitefin dogfish | Japanese : Kasumizame |
| Squaliformes | Somniosidae | Centroscymnus coelolepis | native | Portuguese dogfish | Japanese : Marubara-yumezame |
| Squaliformes | Somniosidae | Centroscymnus owstonii | native | Roughskin dogfish | Japanese : Yumezame |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis argus | native | Peacock hind | Japanese : Aonomehata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis aurantia | native | Golden hind | Japanese : Hanahata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis boenak | native | Chocolate hind | Japanese : Aosujihata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis formosa | native | Bluelined hind | Japanese : Aosujihata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis igarashiensis | native | Garish hind | Japanese : Shimahata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis leopardus | native | Leopard hind | Japanese : Minami-isohata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis microprion | native | Freckled hind | |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis miniata | native | Coral hind | Japanese : Yukatahata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis polleni | native | Harlequin hind | Japanese : Minamihata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis sexmaculata | native | Sixblotch hind | Japanese : Kokuhanhata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis sonnerati | native | Tomato hind | Japanese : Azahata |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis spiloparaea | native | Strawberry hind | Japanese : Akahana |
| Perciformes/Serranoidei | Epinephelidae | Cephalopholis urodeta | native | Darkfin hind | Japanese : Nijihata |
| Carcharhiniformes | Scyliorhinidae | Cephaloscyllium umbratile | native | Blotchy swell shark | Japanese : Nanukazame |
| Eupercaria/misc | Cepolidae | Cepola schlegelii | native | Japanese : Sumitsuki-akatachi | |
| Lophiiformes | Ceratiidae | Ceratias holboelli | native | Kroyer's deep-sea angler fish | Japanese : Biwa-ankô |
| Lophiiformes | Ceratiidae | Ceratias uranoscopus | native | Stargazing seadevil | |
| Myctophiformes | Myctophidae | Ceratoscopelus townsendi | native | Dogtooth lampfish | |
| Myctophiformes | Myctophidae | Ceratoscopelus warmingii | native | Warming's lantern fish | Japanese : Gokô-hadaka |
| Kurtiformes | Apogonidae | Cercamia cladara | native | Frail cardinalfish | |
| Kurtiformes | Apogonidae | Cercamia eremia | native | Glassy cardinalfish | Japanese : Sakura-tenjikudai |
| Mugiliformes | Mugilidae | Cestraeus plicatilis | native | Lobed river mullet | Japanese : Kawa-bora |
| Beryciformes | Cetomimidae | Cetomimus compunctus | native | Japanese : Irezumi-kujira-uo | |
| Gadiformes | Macrouridae | Cetonurus globiceps | native | Globehead grenadier | Japanese : Dango-hige |
| Lamniformes | Cetorhinidae | Cetorhinus maximus | native | Basking shark | Japanese : Ubazame |
| Eupercaria/misc | Scaridae | Cetoscarus ocellatus | native | Spotted parrotfish | |
| Beryciformes | Cetomimidae | Cetostoma regani | native | Pink flabby whalefish | Japanese : Hosomi-kujira-uo |
| Gobiiformes | Gobiidae | Chaenogobius annularis | native | Forktongue goby | Japanese : Agohaze |
| Gobiiformes | Gobiidae | Chaenogobius gulosus | native | Japanese : Dorome | |
| Lophiiformes | Oneirodidae | Chaenophryne draco | native | Smooth dreamer | Japanese : Raduka-ankô |
| Lophiiformes | Oneirodidae | Chaenophryne longiceps | native | Can-opener smoothdream | |
| Tetraodontiformes | Monacanthidae | Chaetodermis penicilligerus | native | Prickly leatherjacket | Japanese : Higehagi |
| Acanthuriformes | Chaetodontidae | Chaetodon adiergastos | native | Philippine butterflyfish | Japanese : Kurakake-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon argentatus | native | Asian butterflyfish | Japanese : Kagami-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon auriga | native | Threadfin butterflyfish | Japanese : Toge-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon auripes | native | Oriental butterflyfish | Japanese : Chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon baronessa | native | Eastern triangular butterflyfish | Japanese : Mikado-chochô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon bennetti | native | Bluelashed butterflyfish | Japanese : Umizuki-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon citrinellus | native | Speckled butterflyfish | Japanese : Goma-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon collare | native | Redtail butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon daedalma | native | Wrought iron butterflyfish | Japanese : Yûzen |
| Acanthuriformes | Chaetodontidae | Chaetodon ephippium | native | Saddle butterflyfish | Japanese : Seguro-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon guentheri | native | Crochet butterflyfish | Japanese : Kokuten-katagi |
| Acanthuriformes | Chaetodontidae | Chaetodon kleinii | native | Sunburst butterflyfish | Japanese : Mizore-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon lineolatus | native | Lined butterflyfish | Japanese : Nise-furai-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon lunula | native | Raccoon butterflyfish | Japanese : Chôhan |
| Acanthuriformes | Chaetodontidae | Chaetodon lunulatus | native | Oval butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon melannotus | native | Blackback butterflyfish | Japanese : Akebono-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon mertensii | native | Mertens' Butterflyfish | Japanese : Benio-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon meyeri | native | Scrawled butterflyfish | Japanese : Ôgi-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon nippon | native | Japanese butterflyfish | Japanese : Shirakodai |
| Acanthuriformes | Chaetodontidae | Chaetodon octofasciatus | native | Eightband butterflyfish | Japanese : Yasuji-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon ornatissimus | native | Ornate butterflyfish | Japanese : Hanaguro-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon oxycephalus | native | Spotnape butterflyfish | |
| Acanthuriformes | Chaetodontidae | Chaetodon plebeius | native | Blueblotch butterflyfish | Japanese : Sumitsuki-tonosamadai |
| Acanthuriformes | Chaetodontidae | Chaetodon punctatofasciatus | native | Spotband butterflyfish | Japanese : Shichisen-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon quadrimaculatus | native | Fourspot butterflyfish | Japanese : Shiten-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon rafflesii | native | Lattice butterflyfish | Japanese : Ami-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon reticulatus | native | Mailed butterflyfish | Japanese : Hakuten-katagi |
| Acanthuriformes | Chaetodontidae | Chaetodon selene | native | Yellow-dotted butterflyfish | Japanese : Tengu-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon semeion | native | Dotted butterflyfish | Japanese : Remon-chôhô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon speculum | native | Mirror butterflyfish | Japanese : Tonosamadai |
| Acanthuriformes | Chaetodontidae | Chaetodon trifascialis | native | Chevron butterflyfish | Japanese : Yarikatagi |
| Acanthuriformes | Chaetodontidae | Chaetodon trifasciatus | native | Melon butterflyfish | Japanese : Misuji-chô-chô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon ulietensis | native | Pacific double-saddle butterflyfish | Japanese : Sudare-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon unimaculatus | native | Teardrop butterflyfish | Japanese : Itten-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon vagabundus | native | Vagabond butterflyfish | Japanese : Fûrai-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon wiebeli | native | Hongkong butterflyfish | Japanese : Tsuki-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Chaetodon xanthurus | native | Pearlscale butterflyfish | Japanese : Amime-chôchô-uo |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus cephalareticulatus | native | ||
| Acanthuriformes | Pomacanthidae | Chaetodontoplus chrysocephalus | native | Orangeface angelfish | Japanese : Akane-kinchakudai |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus melanosoma | native | Black-velvet angelfish | Japanese : Kiheri-kinchakudai |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus mesoleucus | native | Vermiculate angelfish | Japanese : Chirimen-yakko |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus niger | native | Black angelfish | |
| Acanthuriformes | Pomacanthidae | Chaetodontoplus septentrionalis | native | Bluestriped angelfish | Japanese : Kinchakudai |
| Gobiiformes | Gobiidae | Chaeturichthys jeoni | native | Japanese : Yakiin-haze; Japanese : Yakiinhaze; | |
| Gobiiformes | Gobiidae | Chaeturichthys stigmatias | native | Branded goby | English : Branded goby |
| Acropomatiformes | Champsodontidae | Champsodon guentheri | native | Günther's sabre-gills | Japanese : Kuro-wanigisu |
| Acropomatiformes | Champsodontidae | Champsodon longipinnis | native | Japanese : Minami-wanigisu | |
| Acropomatiformes | Champsodontidae | Champsodon pantolepis | native | ||
| Acropomatiformes | Champsodontidae | Champsodon snyderi | native | Japanese : Wanigisu | |
| Anabantiformes | Channidae | Channa argus | introduced | Snakehead | Japanese : Kamuruchi |
| Anabantiformes | Channidae | Channa asiatica | native | Small snakehead | Japanese : Kôtai |
| Anabantiformes | Channidae | Channa maculata | introduced | Blotched snakehead | Japanese : Taiwan-dojô |
| Gonorynchiformes | Chanidae | Chanos chanos | native | Milkfish | Japanese : Sabahii |
| Pleuronectiformes | Bothidae | Chascanopsetta lugubris | native | Pelican flounder | Japanese : Zaragarei |
| Pleuronectiformes | Bothidae | Chascanopsetta micrognatha | native | ||
| Pleuronectiformes | Bothidae | Chascanopsetta prognatha | native | Japanese : Ukeguchi-zaragarei | |
| Anguilliformes | Ophichthidae | Chauligenion camelopardalis | native | Giraffe-spotted snake eel | Japanese : Kirin-umihebi-zoku |
| Stomiiformes | Stomiidae | Chauliodus macouni | native | Pacific viperfish | Japanese : Higashi-hôrai-eso |
| Stomiiformes | Stomiidae | Chauliodus sloani | native | Sloane's viperfish | Japanese : Hôrai-eso |
| Lophiiformes | Chaunacidae | Chaunax abei | native | Japanese : Midori-fusa-ankô | |
| Lophiiformes | Chaunacidae | Chaunax apus | native | ||
| Lophiiformes | Chaunacidae | Chaunax fimbriatus | native | Tassled coffinfish | Japanese : Hon-fusa-ankô |
| Lophiiformes | Chaunacidae | Chaunax penicillatus | native | Pencil coffinfish | Japanese : Hanaguro-fusa-ankô |
| Eupercaria/misc | Labridae | Cheilinus chlorourus | native | Floral wrasse | Japanese : Akaten-mochino-uo |
| Eupercaria/misc | Labridae | Cheilinus fasciatus | native | Redbreasted wrasse | Japanese : Yashabera |
| Eupercaria/misc | Labridae | Cheilinus oxycephalus | native | Red Maori Wrasse | |
| Eupercaria/misc | Labridae | Cheilinus trilobatus | native | Tripletail wrasse | Japanese : Mitsuba-mochino-uo |
| Eupercaria/misc | Labridae | Cheilinus undulatus | native | Humphead wrasse | Japanese : Megane-mochino-uo |
| Eupercaria/misc | Labridae | Cheilio inermis | native | Cigar wrasse | Japanese : Kamasubera |
| Kurtiformes | Apogonidae | Cheilodipterus artus | native | Wolf cardinalfish | |
| Kurtiformes | Apogonidae | Cheilodipterus intermedius | native | Intermediate cardinalfish | Japanese : Sudare-yarai-ishimochi |
| Kurtiformes | Apogonidae | Cheilodipterus macrodon | native | Large toothed cardinalfish | Japanese : Ryukyu-yarai-ishimochi |
| Kurtiformes | Apogonidae | Cheilodipterus quinquelineatus | native | Fiveline cardinalfish | Japanese : Yarai-ishimochi |
| Kurtiformes | Apogonidae | Cheilodipterus subulatus | native | ||
| Beloniformes | Exocoetidae | Cheilopogon agoo | native | Japanese flyingfish | Japanese : Tobi-uo |
| Beloniformes | Exocoetidae | Cheilopogon atrisignis | native | Glider flyingfish | Japanese : Aka-tobi |
| Beloniformes | Exocoetidae | Cheilopogon cyanopterus | native | Margined flyingfish | Japanese : Karasu-tobi-uo |
| Beloniformes | Exocoetidae | Cheilopogon doederleinii | native | Japanese : Tsukushi-tobi-uo | |
| Beloniformes | Exocoetidae | Cheilopogon furcatus | native | Spotfin flyingfish | Japanese : Shirofuchi-tobi-uo |
| Beloniformes | Exocoetidae | Cheilopogon japonicus | native | Japanese : Hama-tobi-uo | |
| Beloniformes | Exocoetidae | Cheilopogon spilonotopterus | native | Stained flyingfish | |
| Beloniformes | Exocoetidae | Cheilopogon spilopterus | native | Manyspotted flyingfish | Japanese : Matô-tobi-uo |
| Beloniformes | Exocoetidae | Cheilopogon suttoni | native | Sutton's flyingfish | Japanese : Ô-aka-tobi |
| Beloniformes | Exocoetidae | Cheilopogon unicolor | native | Limpid-wing flyingfish | Japanese : Ôme-natsu-tobi |
| Ovalentaria/misc | Pomacentridae | Cheiloprion labiatus | native | Big-lip damsel | Japanese : Atsukutchi-suzumedai |
| Perciformes/Scorpaenoidei | Triglidae | Chelidonichthys ischyrus | native | Japanese : Seppari-hôbô | |
| Perciformes/Scorpaenoidei | Triglidae | Chelidonichthys kumu | native | Bluefin gurnard | |
| Perciformes/Scorpaenoidei | Triglidae | Chelidonichthys spinosus | native | Spiny red gurnard | Japanese : Hôbô |
| Perciformes/Serranoidei | Serranidae | Chelidoperca hirundinacea | native | Red blotch perchlet | Japanese : Himekodai |
| Perciformes/Serranoidei | Serranidae | Chelidoperca margaritifera | native | Pearly perchlet | Japanese : Minami-himekodai |
| Perciformes/Serranoidei | Serranidae | Chelidoperca pleurospilus | native | Arafura perchlet | Japanese : Hoshi-himekodai |
| Perciformes/Serranoidei | Serranidae | Chelidoperca santosi | native | Pogi perchlet | |
| Perciformes/Serranoidei | Serranidae | Chelidoperca tosaensis | native | Red-spot perchlet | Japanese : Tosa-himekodai |
| Acanthuriformes | Chaetodontidae | Chelmon rostratus | native | Copperband butterflyfish | Japanese : Hashinagachochô-uo |
| Tetraodontiformes | Tetraodontidae | Chelonodontops patoca | native | Milkspotted puffer | Japanese : Okinawafugu |
| Scombriformes | Chiasmodontidae | Chiasmodon niger | native | Black swallower | Japanese : Oni-bôzugisu |
| Scombriformes | Chiasmodontidae | Chiasmodon pluriradiatus | native | ||
| Tetraodontiformes | Diodontidae | Chilomycterus reticulatus | native | Spotfin burrfish | Japanese : Ishigakifugu |
| Orectolobiformes | Hemiscylliidae | Chiloscyllium plagiosum | native | Whitespotted bambooshark | Japanese : Shiroboshi-tenjiku |
| Orectolobiformes | Hemiscylliidae | Chiloscyllium punctatum | native | Brownbanded bambooshark | Japanese : Inuzame |
| Chimaeriformes | Chimaeridae | Chimaera jordani | native | Japanese : Jordan-ginzame | |
| Chimaeriformes | Chimaeridae | Chimaera owstoni | native | Japanese : Shirobuchi-ginzame | |
| Chimaeriformes | Chimaeridae | Chimaera phantasma | native | Silver chimaera | Japanese : Ginzame |
| Chimaeriformes | Chimaeridae | Chimaera stellata | native | ||
| Clupeiformes | Chirocentridae | Chirocentrus dorab | native | Dorab wolf-herring | Japanese : Oki-iwashi |
| Perciformes/Zoarcoidei | Stichaeidae | Chirolophis japonicus | native | Japanese : Fusaginpo | |
| Perciformes/Zoarcoidei | Stichaeidae | Chirolophis saitone | native | Japanese : Akiginpo | |
| Perciformes/Zoarcoidei | Stichaeidae | Chirolophis snyderi | native | Bearded warbonnet | Japanese : Hanabusaginpo |
| Lophiiformes | Oneirodidae | Chirophryne xenolophus | native | ||
| Hexanchiformes | Chlamydoselachidae | Chlamydoselachus anguineus | native | Frilled shark | Japanese : Rabuka |
| Aulopiformes | Chlorophthalmidae | Chlorophthalmus acutifrons | native | Greeneye | Japanese : Tomo-mehikari |
| Aulopiformes | Chlorophthalmidae | Chlorophthalmus albatrossis | native | Japanese : Aome-eso | |
| Aulopiformes | Chlorophthalmidae | Chlorophthalmus borealis | native | Japanese : Maru-aome-eso | |
| Aulopiformes | Chlorophthalmidae | Chlorophthalmus nigromarginatus | native | Blackedge greeneye | Japanese : Tsumaguro-aome-eso |
| Aulopiformes | Chlorophthalmidae | Chlorophthalmus pectoralis | native | ||
| Eupercaria/misc | Scaridae | Chlorurus bowersi | native | Bower's parrotfish | Japanese : Ômon-hagebudai |
| Eupercaria/misc | Scaridae | Chlorurus frontalis | native | Pacific slopehead parrotfish | Japanese : Oni-hagebudai |
| Eupercaria/misc | Scaridae | Chlorurus japanensis | native | Palecheek parrotfish | Japanese : Shijûkara |
| Eupercaria/misc | Scaridae | Chlorurus microrhinos | native | Steephead parrots | Japanese : Nanyôbudai |
| Eupercaria/misc | Scaridae | Chlorurus oedema | native | Knothead parrotfish | Japanese : Kobubudai |
| Eupercaria/misc | Scaridae | Chlorurus spilurus | native | Pacific bullethead parrotfish | |
| Eupercaria/misc | Labridae | Choerodon anchorago | native | Orange-dotted tuskfish | Japanese : Kusabi-bera |
| Eupercaria/misc | Labridae | Choerodon azurio | native | Azurio tuskfish | Japanese : Ira |
| Eupercaria/misc | Labridae | Choerodon fasciatus | native | Harlequin tuskfish | Japanese : Shichisenbera |
| Eupercaria/misc | Labridae | Choerodon gymnogenys | native | Japanese : Iramokodi | |
| Eupercaria/misc | Labridae | Choerodon japonicus | native | ||
| Eupercaria/misc | Labridae | Choerodon jordani | native | Jordan's tuskfish | Japanese : Kurakakebera |
| Eupercaria/misc | Labridae | Choerodon robustus | native | Robust tuskfish | Japanese : Miyakobera |
| Eupercaria/misc | Labridae | Choerodon schoenleinii | native | Blackspot tuskfish | Japanese : Shirokurabera |
| Syngnathiformes | Syngnathidae | Choeroichthys sculptus | native | Sculptured pipefish | Japanese : Chigoyôji |
| Perciformes/Bembropoidei | Bembropidae | Chrionema chlorotaenia | native | Japanese : Ohaguro-ibaratoragisu | |
| Perciformes/Bembropoidei | Bembropidae | Chrionema chryseres | native | Japanese : Nanyô-ibaratoragisu | |
| Perciformes/Bembropoidei | Bembropidae | Chrionema furunoi | native | Japanese : Ibaratoragisu | |
| Perciformes/Serranoidei | Epinephelidae | Chromileptes altivelis | native | Humpback grouper | Japanese : Sarasa-hata |
| Ovalentaria/misc | Pomacentridae | Chromis albicauda | native | White-caudal chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis albomaculata | native | White-spotted chromis | Japanese : Shiroboshi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis alpha | native | Yellow-speckled chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis anadema | native | Short-tail doublebar Chromis | Japanese : Kanzashi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis analis | native | Yellow chromis | Japanese : Kogane-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis atripectoralis | native | Black-axil chromis | Japanese : Aoba-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis chrysura | native | Stout chromis | Japanese : Amami suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis flavomaculata | native | Yellow-spotted chromis | Japanese : Kihoshi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis fumea | native | Smokey chromis | Japanese : Matsuba-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis mirationis | native | Japanese chromis | Japanese : Tokai-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis notata | native | Pearl-spot chromis | Japanese : Miyake-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis okamurai | native | Okinawa chromis | |
| Ovalentaria/misc | Pomacentridae | Chromis onumai | native | Japanese : Ryusei-suzumedai | |
| Ovalentaria/misc | Pomacentridae | Chromis ternatensis | native | Ternate chromis | Japanese : Kaburaya-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis tingting | native | Moonstone Chromis | Japanese : Gekko-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis viridis | native | Blue green damselfish | Japanese : Deba-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis weberi | native | Weber's chromis | Japanese : Takasago-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis xanthura | native | Paletail chromis | Japanese : Mon-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chromis yamakawai | native | Northern yellow-spotted Chromis | Japanese : Kihoshi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera biocellata | native | Twinspot damselfish | Japanese : Sujibuchi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera brownriggii | native | Surge damselfish | Japanese : Miyakokisen-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera caeruleolineata | native | Blueline demoiselle | Japanese : Aosuji-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera cyanea | native | Sapphire devil | Japanese : Ruri-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera glauca | native | Grey demoiselle | Japanese : Nezu-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera hemicyanea | native | Azure demoiselle | Japanese : Shiriki-ruri-suzume |
| Ovalentaria/misc | Pomacentridae | Chrysiptera parasema | native | Goldtail demoiselle | |
| Ovalentaria/misc | Pomacentridae | Chrysiptera rex | native | King demoiselle | Japanese : Remon-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera starcki | native | Starck's demoiselle | Japanese : Senaki-ruri-suzumedai |
| Ovalentaria/misc | Pomacentridae | Chrysiptera unimaculata | native | Onespot demoiselle | Japanese : Ichimon-suzumedai |
| Squaliformes | Squalidae | Cirrhigaleus barbifer | native | Mandarin dogfish | Japanese : Higetsunozame |
| Eupercaria/misc | Labridae | Cirrhilabrus cyanopleura | native | Blueside wrasse | Japanese : Kuroheri-itohikibera |
| Eupercaria/misc | Labridae | Cirrhilabrus exquisitus | native | Exquisite wrasse | Japanese : Nishiki-itohikibera |
| Eupercaria/misc | Labridae | Cirrhilabrus isosceles | native | Pintail fairy-wrasse | Japanese : Hario-Itohikibera |
| Eupercaria/misc | Labridae | Cirrhilabrus katherinae | native | Katherine's wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus katoi | native | Japanese : Kurenai-itohiki-bera | |
| Eupercaria/misc | Labridae | Cirrhilabrus lanceolatus | native | Long-tailed wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus lunatus | native | ||
| Eupercaria/misc | Labridae | Cirrhilabrus melanomarginatus | native | Blackfin fairy-warsse | |
| Eupercaria/misc | Labridae | Cirrhilabrus rubrimarginatus | native | Red-margined wrasse | |
| Eupercaria/misc | Labridae | Cirrhilabrus ryukyuensis | native | ||
| Eupercaria/misc | Labridae | Cirrhilabrus temminckii | native | Threadfin wrasse | Japanese : Itohikibera |
| Centrarchiformes | Cirrhitidae | Cirrhitichthys aprinus | native | Spotted hawkfish | Japanese : Minamigonbe |
| Centrarchiformes | Cirrhitidae | Cirrhitichthys aureus | native | Yellow hawkfish | Japanese : Thoc |
| Centrarchiformes | Cirrhitidae | Cirrhitichthys falco | native | Dwarf hawkfish | Japanese : Sarasagonbe |
| Centrarchiformes | Cirrhitidae | Cirrhitichthys oxycephalus | native | Coral hawkfish | |
| Centrarchiformes | Cirrhitidae | Cirrhitops fasciatus | native | Redbarred hawkfish | |
| Centrarchiformes | Cirrhitidae | Cirrhitops hubbardi | native | Japanese : Sumitsukigonbe | |
| Centrarchiformes | Cirrhitidae | Cirrhitus pinnulatus | native | Stocky hawkfish | Japanese : Isogonbe |
| Orectolobiformes | Parascylliidae | Cirrhoscyllium expolitum | native | Barbelthroat carpetshark | Japanese : Higezame |
| Orectolobiformes | Parascylliidae | Cirrhoscyllium japonicum | endemic | Saddle carpetshark | Japanese : Kurakakezame |
| Blenniiformes | Blenniidae | Cirripectes castaneus | native | Chestnut eyelash-blenny | Japanese : Tategami-kaeru-uo |
| Blenniiformes | Blenniidae | Cirripectes imitator | native | Imitator blenny | |
| Blenniiformes | Blenniidae | Cirripectes kuwamurai | endemic | Japanese : Suji-tategami-kaeru-uo | |
| Blenniiformes | Blenniidae | Cirripectes polyzona | native | Japanese : Mino-kaeru-uo | |
| Blenniiformes | Blenniidae | Cirripectes quagga | native | Squiggly blenny | |
| Blenniiformes | Blenniidae | Cirripectes stigmaticus | native | Red-streaked blenny | |
| Blenniiformes | Blenniidae | Cirripectes variolosus | native | Red-speckled blenny | Japanese : Benitsuke-tategami-kaeru-uo |
| Pleuronectiformes | Citharidae | Citharoides macrolepidotus | native | Branched ray flounder | Japanese : Kokebirame |
| Siluriformes | Clariidae | Clarias batrachus | introduced | Philippine catfish | |
| Siluriformes | Clariidae | Clarias fuscus | introduced | Hong Kong catfish | Japanese : Hirenamazu |
| Gobiiformes | Gobiidae | Clariger chionomaculatus | native | Japanese : Awayuki-sejiro-haze | |
| Gobiiformes | Gobiidae | Clariger cosmurus | native | Japanese : Sejirohaze | |
| Gobiiformes | Gobiidae | Clariger exilis | native | Japanese : Shimofuri-sejirohaze | |
| Gobiiformes | Gobiidae | Clariger papillosus | native | Japanese : Hige-sejirohaze | |
| Gobiiformes | Gobiidae | Clariger sirahamaensis | endemic | ||
| Pleuronectiformes | Pleuronectidae | Cleisthenes pinetorum | native | Sôhachi | Japanese : Sôhachi |
| Pleuronectiformes | Pleuronectidae | Clidoderma asperrimum | native | Roughscale sole | Japanese : Samegarei |
| Clupeiformes | Clupeidae | Clupea pallasii | native | Pacific herring | Japanese : Nishin |
| Cypriniformes | Cobitidae | Cobitis biwae | native | Japanese : Shima-dojô | |
| Cypriniformes | Cobitidae | Cobitis kaibarai | native | Japanese : Ariake-suji-shima-dojō | |
| Cypriniformes | Cobitidae | Cobitis magnostriata | native | Japanese : Ōgata-suji-shima-dojō | |
| Cypriniformes | Cobitidae | Cobitis matsubarae | native | Japanese : Yamato-shima-dojo | |
| Cypriniformes | Cobitidae | Cobitis minamorii | endemic | Japanese : Biwa-kogata-suji-shima-dojō; Japanese : San'in-kogata-suji-shima-dojō; Japanese : Tōkai-kogata-suji-shima-dojō; | |
| Cypriniformes | Cobitidae | Cobitis sakahoko | native | ||
| Cypriniformes | Cobitidae | Cobitis shikokuensis | native | Japanese : Hina-ishi-dojo | |
| Cypriniformes | Cobitidae | Cobitis striata | native | Japanese : Hakata-suji-shima-dojyô; Japanese : Onga-suji-shima-dojyô; Japanese : Suji-shima-dojô; | |
| Cypriniformes | Cobitidae | Cobitis takatsuensis | endemic | Japanese : Ishi-dojô | |
| Cypriniformes | Cobitidae | Cobitis takenoi | native | ||
| Aulopiformes | Evermannellidae | Coccorella atlantica | native | Atlantic sabretooth | Japanese : Yari-eso |
| Aulopiformes | Evermannellidae | Coccorella atrata | native | Japanese : Minami-yarieso | |
| Perciformes/Scorpaenoidei | Platycephalidae | Cociella crocodilus | native | Crocodile flathead | Japanese : Inegochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Cociella punctata | native | Spotted flathead | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus aurantius | native | ||
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus izuensis | native | Japanese : Izu-okoze | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus keramaensis | native | Japanese : Kerama-okoze | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus larvatus | native | Ghost velvetfish | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus masudai | native | Japanese : Masuda-okoze | |
| Perciformes/Scorpaenoidei | Aploactinidae | Cocotropus possi | native | Japanese : Higemojya-okoze | |
| Lophiiformes | Ogcocephalidae | Coelophrys bradburyae | native | ||
| Lophiiformes | Ogcocephalidae | Coelophrys brevicaudata | native | ||
| Lophiiformes | Ogcocephalidae | Coelophrys micropus | native | ||
| Gadiformes | Macrouridae | Coelorinchus anatirostris | native | Duckbill grenadier | Japanese : Nezumi-hige |
| Gadiformes | Macrouridae | Coelorinchus asteroides | native | Japanese : Hoshi-hige | |
| Gadiformes | Macrouridae | Coelorinchus formosanus | native | Formosa grenadier | Japanese : Taiwan-sokodara |
| Gadiformes | Macrouridae | Coelorinchus gilberti | native | Japanese : Oni-hige | |
| Gadiformes | Macrouridae | Coelorinchus hexafasciatus | native | Six-band grenadier | Japanese : Musuji-sokodara |
| Gadiformes | Macrouridae | Coelorinchus hige | native | ||
| Gadiformes | Macrouridae | Coelorinchus hubbsi | native | Japanese : Moyô-hige | |
| Gadiformes | Macrouridae | Coelorinchus japonicus | native | Japanese grenadier | Japanese : Tôjin |
| Gadiformes | Macrouridae | Coelorinchus jordani | native | Japanese : Kyushu-hige | |
| Gadiformes | Macrouridae | Coelorinchus kamoharai | native | Kamohara grenadier | Japanese : Ichimonji-hige |
| Gadiformes | Macrouridae | Coelorinchus kishinouyei | native | Mugura grenadier | Japanese : Mugura-hige |
| Gadiformes | Macrouridae | Coelorinchus lanceolatus | native | Japanese : Yajirihige | |
| Gadiformes | Macrouridae | Coelorinchus longicephalus | native | Longhead grenadier | Japanese : Zunaga-sokodara |
| Gadiformes | Macrouridae | Coelorinchus longissimus | native | Japanese : Tongari-hige | |
| Gadiformes | Macrouridae | Coelorinchus macrochir | native | Longarm grenadier | Japanese : Tenagadara |
| Gadiformes | Macrouridae | Coelorinchus matsubarai | native | Japanese : Matô-hige | |
| Gadiformes | Macrouridae | Coelorinchus multispinulosus | native | Spearnose grenadier | Japanese : Yari-hige |
| Gadiformes | Macrouridae | Coelorinchus nox | native | Japanese : Yami-hige | |
| Gadiformes | Macrouridae | Coelorinchus parallelus | native | Spiny grenadier | Japanese : Soroi-hige |
| Gadiformes | Macrouridae | Coelorinchus productus | native | Unicorn grenadier | Japanese : Tengu-hige |
| Gadiformes | Macrouridae | Coelorinchus smithi | native | False graceful whiptail | Japanese : Kishû-hige |
| Gadiformes | Macrouridae | Coelorinchus tokiensis | native | Japanese : Miyako-hige | |
| Clupeiformes | Engraulidae | Coilia nasus | native | Japanese grenadier anchovy | Japanese : Etsu |
| Eupercaria/misc | Sciaenidae | Collichthys lucidus | native | Japanese : Kandari | |
| Anguilliformes | Colocongridae | Coloconger japonicus | native | Japanese : Bake-fusa-anago | |
| Anguilliformes | Colocongridae | Coloconger raniceps | native | Froghead eel | Japanese : Fusa-anago |
| Beloniformes | Scomberesocidae | Cololabis saira | native | Pacific saury | Japanese : Sanma |
| Anguilliformes | Congridae | Conger cinereus | native | Longfin African conger | Japanese : Kiri-anago |
| Anguilliformes | Congridae | Conger erebennus | native | Japanese : Dainan-anago | |
| Anguilliformes | Congridae | Conger japonicus | native | Beach conger | Japanese : Kuro-anago |
| Anguilliformes | Congridae | Conger jordani | native | ||
| Anguilliformes | Congridae | Conger myriaster | native | Whitespotted conger | Japanese : Ma-anago |
| Anguilliformes | Congridae | Congriscus megastoma | native | Japanese : Oki-anago | |
| Ovalentaria/misc | Pseudochromidae | Congrogadus subducens | native | Carpet eel-blenny | Japanese : Sen-ningaji |
| Gobiesociformes | Gobiesocidae | Conidens laticephalus | native | Broadhead clingfish | Japanese : Ankô-uba-uo |
| Eupercaria/misc | Priacanthidae | Cookeolus japonicus | native | Longfinned bullseye | |
| Cichliformes | Cichlidae | Coptodon zillii | introduced | Redbelly tilapia | Japanese : Jiru-tirapia |
| Acanthuriformes | Chaetodontidae | Coradion altivelis | native | Highfin coralfish | Japanese : Takigenrokudai |
| Acanthuriformes | Chaetodontidae | Coradion chrysozonus | native | Goldengirdled coralfish | Japanese : Kisujigenrokudai |
| Salmoniformes | Salmonidae | Coregonus lavaretus | introduced | European whitefish | |
| Salmoniformes | Salmonidae | Coregonus maraena | introduced | Maraena whitefish | |
| Siluriformes | Bagridae | Coreobagrus ichikawai | endemic | Neko-gigi | Japanese : Nekogigi |
| Centrarchiformes | Sinipercidae | Coreoperca kawamebari | native | Japanese : Oyanirami | |
| Eupercaria/misc | Labridae | Coris aygula | native | Clown coris | Japanese : Kanmuribera |
| Eupercaria/misc | Labridae | Coris batuensis | native | Batu coris | Japanese : Shichisen-musumebera |
| Eupercaria/misc | Labridae | Coris dorsomacula | native | Pale-barred coris | Japanese : Sujibera |
| Eupercaria/misc | Labridae | Coris gaimard | native | African coris | Japanese : Tsuyubera |
| Eupercaria/misc | Labridae | Coris musume | native | Japanese : Musumebera | |
| Eupercaria/misc | Labridae | Coris picta | native | Comb wrasse | |
| Carangiformes | Coryphaenidae | Coryphaena equiselis | native | Pompano dolphinfish | Japanese : Ebisu-shiira |
| Carangiformes | Coryphaenidae | Coryphaena hippurus | native | Common dolphinfish | Japanese : Shiira |
| Gadiformes | Macrouridae | Coryphaenoides acrolepis | native | Pacific grenadier | Japanese : Ibara-hige |
| Gadiformes | Macrouridae | Coryphaenoides altipinnis | native | Japanese : Hokakedara | |
| Gadiformes | Macrouridae | Coryphaenoides asper | native | Japanese : Zaradara | |
| Gadiformes | Macrouridae | Coryphaenoides cinereus | native | Popeye grenadier | Japanese : Karafuto-sokodara |
| Gadiformes | Macrouridae | Coryphaenoides filamentosus | native | Japanese : Hokuyô-sokodara | |
| Gadiformes | Macrouridae | Coryphaenoides liocephalus | native | Bearded rattail | Japanese : Hiragashiradara |
| Gadiformes | Macrouridae | Coryphaenoides longifilis | native | Longfin grenadier | Japanese : Himodara |
| Gadiformes | Macrouridae | Coryphaenoides marginatus | native | Amami grenadier | Japanese : Heridara |
| Gadiformes | Macrouridae | Coryphaenoides microps | native | ||
| Gadiformes | Macrouridae | Coryphaenoides nasutus | native | Largenose grenadier | Japanese : Hana-sokodara |
| Gadiformes | Macrouridae | Coryphaenoides soyoae | native | Black grenadier | Japanese : Kuro-hige |
| Gadiformes | Macrouridae | Coryphaenoides yaquinae | native | Japanese : Shinkaiyoroi-dara | |
| Syngnathiformes | Syngnathidae | Corythoichthys amplexus | native | Brown-banded pipefish | Japanese : Obi-ishi-yôji |
| Syngnathiformes | Syngnathidae | Corythoichthys flavofasciatus | native | Network pipefish | Japanese : Kishima-ishi-yôji |
| Syngnathiformes | Syngnathidae | Corythoichthys haematopterus | native | Messmate pipefish | Japanese : Ishi-yôji |
| Syngnathiformes | Syngnathidae | Corythoichthys schultzi | native | Schultz's pipefish | Japanese : Kuchinaga-ishi-yôji |
| Syngnathiformes | Syngnathidae | Cosmocampus banneri | native | Roughridge pipefish | |
| Perciformes/Cottoidei | Cottidae | Cottiusculus gonez | native | Japanese : Okihimekajika | |
| Perciformes/Cottoidei | Cottidae | Cottiusculus nihonkaiensis | native | Japanese : Nihon-kin-kajika | |
| Perciformes/Cottoidei | Cottidae | Cottiusculus schmidti | native | Japanese : Kinkajika | |
| Perciformes/Cottoidei | Cottidae | Cottus amblystomopsis | native | Sakhalin sculpin | Japanese : Ezohana-kajika |
| Perciformes/Cottoidei | Cottidae | Cottus czerskii | native | Cherskii's sculpin | |
| Perciformes/Cottoidei | Cottidae | Cottus hangiongensis | native | Japanese : Kankyo-kajika | |
| Perciformes/Cottoidei | Cottidae | Cottus kazika | native | Fourspine sculpin | Japanese : Kamakiri |
| Perciformes/Cottoidei | Cottidae | Cottus nozawae | native | Japanese : Hana-kajika | |
| Perciformes/Cottoidei | Cottidae | Cottus pollux | native | Japanese fluvial sculpin | Japanese : Kajika |
| Perciformes/Cottoidei | Cottidae | Cottus reinii | native | Japanese : Utsusemi-kajika | |
| Torpediniformes | Narkidae | Crassinarke dormitor | native | Sleeper torpedo | Japanese : Nemuri-shibire-ei |
| Carangiformes | Carangidae | Craterognathus plagiotaenia | native | Barcheek trevally | Japanese : Indo-kaiwari |
| Gobiiformes | Gobiidae | Cristatogobius aurimaculatus | native | Japanese : Hime-tosakahaze | |
| Gobiiformes | Gobiidae | Cristatogobius lophius | native | Japanese : Tosakahaze | |
| Gobiiformes | Gobiidae | Cristatogobius nonatoae | native | Japanese : Kuro-tosakahaze | |
| Pleuronectiformes | Bothidae | Crossorhombus kanekonis | native | Japanese : Kanekodarumagarei | |
| Pleuronectiformes | Bothidae | Crossorhombus kobensis | native | Kobe flounder | Japanese : Kôbedarumagarei |
| Pleuronectiformes | Bothidae | Crossorhombus valderostratus | native | Broadbrow flounder | |
| Blenniiformes | Blenniidae | Crossosalarias macrospilus | native | Tripplespot blenny | Japanese : Eriguroginpo |
| Perciformes/Zoarcoidei | Cryptacanthodidae | Cryptacanthodes bergi | native | English : Berg wrymouth | |
| Gobiiformes | Gobiidae | Cryptocentroides insignis | native | Insignia prawn-goby | Japanese : Hasujimahaze |
| Gobiiformes | Gobiidae | Cryptocentrus albidorsus | native | White-backed shrimpgoby | Japanese : Shiro-obihaze |
| Gobiiformes | Gobiidae | Cryptocentrus caeruleomaculatus | native | Blue-speckled prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus cinctus | native | Yellow prawn-goby | Japanese : Gingahaze |
| Gobiiformes | Gobiidae | Cryptocentrus flavus | native | Japanese : Koganehaze | |
| Gobiiformes | Gobiidae | Cryptocentrus inexplicatus | native | Inexplicable shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus leptocephalus | native | Pink-speckled shrimpgoby | Japanese : Oiranhaze |
| Gobiiformes | Gobiidae | Cryptocentrus leucostictus | native | Saddled prawn-goby | |
| Gobiiformes | Gobiidae | Cryptocentrus nigrocellatus | native | Blackspot shrimpgoby | Japanese : Kurohoshihaze |
| Gobiiformes | Gobiidae | Cryptocentrus octofasciatus | native | Blue-speckled prawn goby | Japanese : Takanohahaze |
| Gobiiformes | Gobiidae | Cryptocentrus sericus | native | Ventral-barred shrimpgoby | |
| Gobiiformes | Gobiidae | Cryptocentrus shigensis | native | Shige shrimpgoby | Japanese : Shigehaze |
| Gobiiformes | Gobiidae | Cryptocentrus strigilliceps | native | Target shrimp goby | Japanese : Hinomaruhaze |
| Lophiiformes | Ceratiidae | Cryptopsaras couesii | native | Triplewart seadevil | Japanese : Mitsukuri-enagachôchin-ankô |
| Perciformes/Cottoidei | Liparidae | Crystallias matsushimae | native | Japanese : Abachan | |
| Acanthuriformes | Acanthuridae | Ctenochaetus binotatus | native | Twospot surgeonfish | Japanese : Kokuten-sazanamihagi |
| Acanthuriformes | Acanthuridae | Ctenochaetus hawaiiensis | native | Chevron tang | |
| Acanthuriformes | Acanthuridae | Ctenochaetus striatus | native | Striated surgeonfish | Japanese : Sazanamihagi |
| Gobiiformes | Gobiidae | Ctenogobiops aurocingulus | native | Gold-streaked prawn-goby | Japanese : Obi-shinobihaze |
| Gobiiformes | Gobiidae | Ctenogobiops crocineus | native | Japanese : Hohosuji-shinobihaze | |
| Gobiiformes | Gobiidae | Ctenogobiops feroculus | native | Sandy prawn-goby | Japanese : Hime-shinobihaze |
| Gobiiformes | Gobiidae | Ctenogobiops pomastictus | native | Gold-specked prawn-goby | Japanese : Shinobihaze |
| Gobiiformes | Gobiidae | Ctenogobiops tangaroai | native | Tangaroa shrimpgoby | Japanese : Hatatate-shinobihaze |
| Cypriniformes | Xenocyprididae | Ctenopharyngodon idella | introduced | Grass carp | Japanese : Sôgyo |
| Scombriformes | Nomeidae | Cubiceps baxteri | native | Black fathead | Japanese : Okimedai |
| Scombriformes | Nomeidae | Cubiceps pauciradiatus | native | Bigeye cigarfish | Japanese : Hoso-okimedai |
| Scombriformes | Nomeidae | Cubiceps whiteleggii | native | Shadow driftfish | Japanese : Bouzu-konnyaku |
| Tetraodontiformes | Diodontidae | Cyclichthys orbicularis | native | Birdbeak burrfish | Japanese : Meita Ishigakifugu |
| Tetraodontiformes | Diodontidae | Cyclichthys spilostylus | native | Spotbase burrfish | |
| Perciformes/Cottoidei | Cyclopteridae | Cyclopsis tentacularis | native | ||
| Perciformes/Cottoidei | Cyclopteridae | Cyclopteropsis bergi | native | Japanese : Kobu-fûsen-uo | |
| Stomiiformes | Gonostomatidae | Cyclothone acclinidens | native | Benttooth bristlemouth | Japanese : Sen-oni-hadaka |
| Stomiiformes | Gonostomatidae | Cyclothone alba | native | Bristlemouth | Japanese : Yuki-oni-hadaka |
| Stomiiformes | Gonostomatidae | Cyclothone atraria | native | Deep-water bristlemouth | Japanese : Oni-hadaka |
| Stomiiformes | Gonostomatidae | Cyclothone obscura | native | Hidden bristlemouth | |
| Stomiiformes | Gonostomatidae | Cyclothone pallida | native | Tan bristlemouth | Japanese : Usu-oni-hadaka |
| Stomiiformes | Gonostomatidae | Cyclothone pseudopallida | native | Slender bristlemouth | Japanese : Haiiro-oni-hadaka |
| Saccopharyngiformes | Cyematidae | Cyema atrum | native | Bobtail eel | |
| Perciformes/Scorpaenoidei | Platycephalidae | Cymbacephalus beauforti | native | Crocodile fish | |
| Eupercaria/misc | Labridae | Cymolutes torquatus | native | Finescale razorfish | Japanese : Tateyamabera |
| Pleuronectiformes | Cynoglossidae | Cynoglossus abbreviatus | native | Three-lined tongue sole | Japanese : Kourai-aka-shita-birame |
| Pleuronectiformes | Cynoglossidae | Cynoglossus arel | native | Largescale tonguesole | Japanese : Tenjiku-inunoshita |
| Pleuronectiformes | Cynoglossidae | Cynoglossus bilineatus | native | Fourlined tonguesole | Japanese : Ôshitabirame |
| Pleuronectiformes | Cynoglossidae | Cynoglossus interruptus | native | Genko sole | Japanese : Genko |
| Pleuronectiformes | Cynoglossidae | Cynoglossus itinus | native | Speckled tongue sole | Japanese : Minami-akashitabirame |
| Pleuronectiformes | Cynoglossidae | Cynoglossus joyneri | native | Red tonguesole | Japanese : Akashitabirame |
| Pleuronectiformes | Cynoglossidae | Cynoglossus nigropinnatus | native | Japanese : Hireguro-genko | |
| Pleuronectiformes | Cynoglossidae | Cynoglossus ochiaii | native | Japanese : Oki-genko | |
| Pleuronectiformes | Cynoglossidae | Cynoglossus purpureomaculatus | native | ||
| Pleuronectiformes | Cynoglossidae | Cynoglossus robustus | native | Japanese : Inunoshita | |
| Pleuronectiformes | Cynoglossidae | Cynoglossus yokomaru | native | High-forehead genko sole | Japanese : Otafuku-genko |
| Centrarchiformes | Cirrhitidae | Cyprinocirrhites polyactis | native | Swallowtail hawkfish | Japanese : Uigonbe |
| Cypriniformes | Cyprinidae | Cyprinus carpio | introduced | Common carp | Japanese : Koi |
| Beloniformes | Exocoetidae | Cypselurus angusticeps | native | Narrowhead flyingfish | Japanese : Hime-akatobi |
| Beloniformes | Exocoetidae | Cypselurus hiraii | native | Japanese : Hoso-tobi-uo | |
| Beloniformes | Exocoetidae | Cypselurus longibarbus | native | ||
| Beloniformes | Exocoetidae | Cypselurus naresii | native | Pharao flyingfish | Japanese : Uchida-tobi-uo |
| Beloniformes | Exocoetidae | Cypselurus opisthopus | native | Black-finned flyingfish | |
| Beloniformes | Exocoetidae | Cypselurus poecilopterus | native | Yellow-wing flyingfish | Japanese : Aya-tobi-uo |
| Beloniformes | Exocoetidae | Cypselurus starksi | native | Japanese : Ariake-tobi-uo | |
| Zeiformes | Zeniontidae | Cyttomimus affinis | native | False dory | Japanese : Ao-matôdai |
| Zeiformes | Parazenidae | Cyttopsis rosea | native | Rosy dory | Japanese : Kago-matôdai |
| Dactylopteriformes | Dactylopteridae | Dactyloptena gilberti | native | Japanese : Oki-semihôbô | |
| Dactylopteriformes | Dactylopteridae | Dactyloptena orientalis | native | Oriental flying gurnard | Japanese : Semihôbô |
| Dactylopteriformes | Dactylopteridae | Dactyloptena peterseni | native | Starry flying gurnard | Japanese : Hoshi-semihôbô |
| Callionymiformes | Callionymidae | Dactylopus dactylopus | native | Fingered dragonet | Japanese : Ippon-teguri |
| Squaliformes | Dalatiidae | Dalatias licha | native | Kitefin shark | Japanese : Yoroizame |
| Cypriniformes | Danionidae | Danio albolineatus | introduced | Pearl danio | |
| Cypriniformes | Danionidae | Danio rerio | introduced | Zebra danio | |
| Perciformes/Cottoidei | Cottidae | Daruma sagamia | native | Japanese : Darumakajika | |
| Ovalentaria/misc | Pomacentridae | Dascyllus aruanus | native | Whitetail dascyllus | Japanese : Misuji-ryukyusuzumedai |
| Ovalentaria/misc | Pomacentridae | Dascyllus melanurus | native | Blacktail humbug | Japanese : Yosuji-ryukyusuzumedai |
| Ovalentaria/misc | Pomacentridae | Dascyllus reticulatus | native | Reticulate dascyllus | Japanese : Futasuji-ryukyusuzumedai |
| Ovalentaria/misc | Pomacentridae | Dascyllus trimaculatus | native | Threespot dascyllus | Japanese : Mitsuboshi-kurosuzumedai |
| Perciformes/Cottoidei | Psychrolutidae | Dasycottus setiger | native | Spinyhead sculpin | Japanese : Ganko |
| Myctophiformes | Myctophidae | Dasyscopelus asper | native | Prickly lanternfish | Japanese : Ara-hadaka |
| Myctophiformes | Myctophidae | Dasyscopelus obtusirostris | native | Bluntsnout lanternfish | Japanese : Hisahadaka |
| Myctophiformes | Myctophidae | Dasyscopelus selenops | native | Wisner's lantern fish | Japanese : Hishi-hadaka |
| Myctophiformes | Myctophidae | Dasyscopelus spinosus | native | Spiny lantern fish | Japanese : Ibara-hadaka |
| Perciformes/Zoarcoidei | Zoarcidae | Davidijordania brachyrhynchus | native | Japanese : Nirami-sarasagaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Davidijordania jordaniana | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Davidijordania lacertina | native | Japanese : Naga-sarasagaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Davidijordania poecilimon | native | Japanese : Hime-sarasagaji; Japanese : Sarasagaji; | |
| Perciformes/Zoarcoidei | Zoarcidae | Davidijordania yabei | native | Japanese : Kurakake-sarasagaji | |
| Squaliformes | Centrophoridae | Deania calceus | native | Birdbeak dogfish | Japanese : Heratsunozame |
| Squaliformes | Centrophoridae | Deania hystricosa | native | Rough longnose dogfish | |
| Carangiformes | Carangidae | Decapterus akaadsi | native | Japanese : Aka-aji | |
| Carangiformes | Carangidae | Decapterus kurroides | native | Redtail scad | Japanese : Aka-aji |
| Carangiformes | Carangidae | Decapterus macarellus | native | Mackerel scad | Japanese : Kusaya-moro |
| Carangiformes | Carangidae | Decapterus macrosoma | native | Shortfin scad | Japanese : Moro |
| Carangiformes | Carangidae | Decapterus maruadsi | native | Japanese scad | Japanese : Maru-aji |
| Carangiformes | Carangidae | Decapterus muroadsi | native | Amberstripe scad | Japanese : Muro-aji |
| Carangiformes | Carangidae | Decapterus russelli | native | Indian scad | Japanese : Indo-maruaji |
| Carangiformes | Carangidae | Decapterus tabl | native | Roughear scad | Japanese : Oaka-muro |
| Eupercaria/misc | Labridae | Decodon pacificus | native | Ten-tooth wrasse | Japanese : Kazari-akabô |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus bellus | native | Butterfly scorpionfish | Japanese : Hime-yamanokami |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus biocellatus | native | Twospot turkeyfish | Japanese : Hireboshi-minokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus brachypterus | native | Dwarf lionfish | Japanese : Shimahime-yamanokami |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus koyo | native | Ogasawara dwarf-lionfsh | Japanese : Shiro-himeyamanokami |
| Perciformes/Scorpaenoidei | Scorpaenidae | Dendrochirus zebra | native | Zebra turkeyfish | Japanese : Minokasago |
| Eupercaria/misc | Sparidae | Dentex abei | native | Yellowfin sea bream | Japanese : Kibire-akarenko |
| Eupercaria/misc | Sparidae | Dentex hypselosomus | native | Yellowback sea-bream | Japanese : Kidai |
| Lampriformes | Trachipteridae | Desmodema polystictum | native | Polka-dot ribbonfish | Japanese : Furisode-uo |
| Pleuronectiformes | Pleuronectidae | Dexistes rikuzenius | native | Rikuzen flounder | Japanese : Migigarei |
| Gobiesociformes | Gobiesocidae | Diademichthys lineatus | native | Striped clingfish | Japanese : Hashinaga-uba-uo |
| Eupercaria/misc | Haemulidae | Diagramma pictum | native | Painted sweetlips | Japanese : Korodai |
| Ophidiiformes | Dinematichthyidae | Diancistrus erythraeus | native | Red viviparous brotula | Japanese : Toge-itachiuo |
| Ophidiiformes | Dinematichthyidae | Diancistrus fuscus | native | Dusky brotulid | Japanese : Ryukyu-itachiuo |
| Myctophiformes | Myctophidae | Diaphus adenomus | native | Gilbert's large lantern fish | Japanese : Me-hadaka |
| Myctophiformes | Myctophidae | Diaphus aliciae | native | Japanese : Nirami-hadaka | |
| Myctophiformes | Myctophidae | Diaphus anderseni | native | Andersen's lantern fish | Japanese : Futatsuboshi-hadaka |
| Myctophiformes | Myctophidae | Diaphus bertelseni | native | Bertelsen's lanternfish | Japanese : Tokkuri-hadaka |
| Myctophiformes | Myctophidae | Diaphus brachycephalus | native | Short-headed lantern fish | Japanese : Ebisu-hadaka |
| Myctophiformes | Myctophidae | Diaphus fragilis | native | Fragile lantern fish | Japanese : Kumadori-hadaka |
| Myctophiformes | Myctophidae | Diaphus fulgens | native | Japanese : Kobito-hadaka | |
| Myctophiformes | Myctophidae | Diaphus garmani | native | Garman's lanternfish | Japanese : Hiro-hadaka |
| Myctophiformes | Myctophidae | Diaphus gigas | native | Japanese : Suitô-hadaka | |
| Myctophiformes | Myctophidae | Diaphus jenseni | native | Jensen's lanternfish | Japanese : Chibi-hadaka |
| Myctophiformes | Myctophidae | Diaphus kuroshio | native | Japanese : Kuroshio-hadaka | |
| Myctophiformes | Myctophidae | Diaphus luetkeni | native | Luetken's lanternfish | Japanese : Ganten-hadaka |
| Myctophiformes | Myctophidae | Diaphus malayanus | native | Malayan lanternfish | Japanese : Hanare-hadaka |
| Myctophiformes | Myctophidae | Diaphus metopoclampus | native | Spothead lantern fish | Japanese : Daikoku-hadaka |
| Myctophiformes | Myctophidae | Diaphus mollis | native | Soft lanternfish | Japanese : Otome-hadaka |
| Myctophiformes | Myctophidae | Diaphus nielseni | native | Japanese : Tsukushi-hadaka | |
| Myctophiformes | Myctophidae | Diaphus parri | native | Parr's lanternfish | Japanese : Chikame-hadaka |
| Myctophiformes | Myctophidae | Diaphus perspicillatus | native | Transparent lantern fish | |
| Myctophiformes | Myctophidae | Diaphus phillipsi | native | Bolin's lantern fish | Japanese : Chigire-hadaka |
| Myctophiformes | Myctophidae | Diaphus problematicus | native | Problematic lanternfish | Japanese : Mayoi-hadaka |
| Myctophiformes | Myctophidae | Diaphus regani | native | Regan's lanternfish | Japanese : Agari-hadaka |
| Myctophiformes | Myctophidae | Diaphus richardsoni | native | Japanese : Miho-hadaka | |
| Myctophiformes | Myctophidae | Diaphus sagamiensis | native | Japanese : Sagami-hadaka | |
| Myctophiformes | Myctophidae | Diaphus schmidti | native | Japanese : Taka-hadaka | |
| Myctophiformes | Myctophidae | Diaphus signatus | native | Japanese : Bô-hadaka | |
| Myctophiformes | Myctophidae | Diaphus splendidus | native | Horned lanternfish | Japanese : Tsuno-hadaka |
| Myctophiformes | Myctophidae | Diaphus suborbitalis | native | Japanese : Sen-hadaka | |
| Myctophiformes | Myctophidae | Diaphus watasei | native | Watases lanternfish | Japanese : Hadaka-iwashi |
| Lophiiformes | Ogcocephalidae | Dibranchus japonicus | native | Japanese seabat | Japanese : Soko-gutsu |
| Lophiiformes | Diceratiidae | Diceratias bispinosus | native | Two-rod anglerfish | |
| Lophiiformes | Diceratiidae | Diceratias trilobus | native | ||
| Ophidiiformes | Ophidiidae | Dicrolene quinquarius | native | Japanese : Momo-itachiuo | |
| Ophidiiformes | Ophidiidae | Dicrolene tristis | native | Japanese : Tôyô-momo-itachiuo | |
| Perciformes/Zoarcoidei | Stichaeidae | Dictyosoma burgeri | native | Japanese : Dainanginpo | |
| Perciformes/Zoarcoidei | Stichaeidae | Dictyosoma rubrimaculatum | native | Japanese : Benitsukeginpo | |
| Ophidiiformes | Dinematichthyidae | Dinematichthys iluocoeteoides | native | Yellow pigmy brotula | |
| Tetraodontiformes | Diodontidae | Diodon eydouxii | native | Pelagic porcupinefish | Japanese : Yase-harisenbon |
| Tetraodontiformes | Diodontidae | Diodon holocanthus | native | Longspined porcupinefish | Japanese : Harisenbon |
| Tetraodontiformes | Diodontidae | Diodon hystrix | native | Spot-fin porcupinefish | Japanese : Nezumifugu |
| Tetraodontiformes | Diodontidae | Diodon liturosus | native | Black-blotched porcupinefish | Japanese : Hitozura-harisenbon |
| Myctophiformes | Myctophidae | Diogenichthys atlanticus | native | Longfin lanternfish | Japanese : Ita-hadaka |
| Ophidiiformes | Bythitidae | Diplacanthopoma japonicum | native | Japanese : Bora-itachiuo | |
| Callionymiformes | Callionymidae | Diplogrammus goramensis | native | Goram dragonet | Japanese : Minami-kobunumeri |
| Callionymiformes | Callionymidae | Diplogrammus xenicus | native | Japanese fold dragonet | Japanese : Kobu-numeri |
| Stomiiformes | Gonostomatidae | Diplophos orientalis | native | Japanese : Yumehadaka | |
| Stomiiformes | Gonostomatidae | Diplophos taenia | native | Pacific portholefish | Japanese : Nettai-yumehadaka |
| Perciformes/Serranoidei | Liopropomatidae | Diploprion bifasciatum | native | Barred soapfish | Japanese : Kihassoku |
| Scombriformes | Gempylidae | Diplospinus multistriatus | native | Striped escolar | Japanese : Hoso-kurotachi |
| Rajiformes | Rajidae | Dipturus gigas | native | Giant skate | Japanese : Zôkasube |
| Rajiformes | Rajidae | Dipturus kwangtungensis | native | Kwangtung skate | Japanese : Gangi-ei |
| Rajiformes | Rajidae | Dipturus macrocauda | native | Bigtail skate | Japanese : Kitsunekasube |
| Rajiformes | Rajidae | Dipturus tengu | native | Acutenose skate | Japanese : Tengukasube |
| Trachichthyiformes | Diretmidae | Diretmichthys parini | native | Parin's spinyfish | Japanese : Nakamuraginme |
| Ovalentaria/misc | Pomacentridae | Dischistodus melanotus | native | Blackvent damsel | Japanese : Seguro-suzumedai |
| Ovalentaria/misc | Pomacentridae | Dischistodus prosopotaenia | native | Honeyhead damsel | Japanese : Dandara-suzumedai |
| Gobiiformes | Gobiidae | Discordipinna filamentosa | native | Japanese : Naginata-haze | |
| Gobiiformes | Gobiidae | Discordipinna griessingeri | native | Spikefin goby | Japanese : Homura-haze |
| Gobiesociformes | Gobiesocidae | Discotrema crinophilum | native | Crinoid clingfish | Japanese : Umishida-uba-uo |
| Ovalentaria/misc | Embiotocidae | Ditrema jordani | native | Japanese : Aka-tanago | |
| Ovalentaria/misc | Embiotocidae | Ditrema temminckii | native | English : Temminck's surfperch | |
| Ovalentaria/misc | Embiotocidae | Ditrema viride | native | Japanese : Aotanago | |
| Acropomatiformes | Acropomatidae | Doederleinia berycoides | native | Blackthroat seaperch | Japanese : Akamutsu |
| Argentiniformes | Bathylagidae | Dolicholagus longirostris | native | Longsnout blacksmelt | Japanese : Gin-soko-iwashi |
| Argentiniformes | Opisthoproctidae | Dolichopteryx minuscula | native | Japanese : Hina-deme-nigisu | |
| Argentiniformes | Opisthoproctidae | Dolichopteryx parini | native | Winged spookfish | |
| Lophiiformes | Oneirodidae | Dolopichthys longicornis | native | ||
| Syngnathiformes | Syngnathidae | Doryrhamphus excisus | native | Bluestripe pipefish | Japanese : Hibashi-yôji |
| Syngnathiformes | Syngnathidae | Doryrhamphus japonicus | native | Honshu pipefish | Japanese : Nokogiri-yôji |
| Syngnathiformes | Syngnathidae | Doryrhamphus melanopleura | native | ||
| Syngnathiformes | Syngnathidae | Doryrhamphus negrosensis | native | Negros pipefish | Japanese : Sesuji-yôji |
| Gobiiformes | Gobiidae | Dotsugobius bleekeri | native | Dark mangrovegoby | Japanese : Kumanoko-haze |
| Callionymiformes | Draconettidae | Draconetta xenica | native | Highfin slope dragonet | Japanese : Inaka-numeri |
| Callionymiformes | Callionymidae | Draculo mirabilis | native | Wonder dragonet | Japanese : Bake-numeri |
| Acanthuriformes | Drepaneidae | Drepane longimana | native | Concertina fish | Japanese : Sudaredai |
| Acanthuriformes | Drepaneidae | Drepane punctata | native | Spotted sicklefish | Japanese : Yûdachi-sudaredai |
| Gobiiformes | Gobiidae | Drombus ocyurus | native | Bluemarked drombus | |
| Syngnathiformes | Syngnathidae | Dunckerocampus dactyliophorus | native | Ringed pipefish | Japanese : Oiran-yôji |
| Syngnathiformes | Syngnathidae | Dunckerocampus naia | native | Naia pipefish | |
| Scombriformes | Chiasmodontidae | Dysalotus alcocki | native | ||
| Anguilliformes | Synaphobranchidae | Dysomma anguillare | native | Shortbelly eel | Japanese : Mekura-anago |
| Anguilliformes | Synaphobranchidae | Dysommina orientalis | native | Oriental arrowtooth eel | Japanese : Suruga-anago |
| Perciformes/Cottoidei | Psychrolutidae | Ebinania brephocephala | native | Japanese : Bôzukajika | |
| Perciformes/Cottoidei | Psychrolutidae | Ebinania vermiculata | native | Japanese : Akadonko | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Ebosia bleekeri | native | Bleeker's lionfish | Japanese : Eboshikasago |
| Anguilliformes | Ophichthidae | Echelus uropterus | native | Finned worm eel | Japanese : Hire-anago |
| Carangiformes | Echeneidae | Echeneis naucrates | native | Live sharksucker | Japanese : Kobanzame |
| Anguilliformes | Muraenidae | Echidna delicatula | native | Mottled moray | Japanese : Arashi-utsubo |
| Anguilliformes | Muraenidae | Echidna nebulosa | native | Starry moray | Japanese : Kumo-utsubo |
| Anguilliformes | Muraenidae | Echidna polyzona | native | Barred moray | Japanese : Shima-arashi-utsubo |
| Gobiiformes | Gobiidae | Echinogobius hayashii | native | Cheek-streaked goby | Japanese : Moyoushinobi-haze |
| Echinorhiniformes | Echinorhinidae | Echinorhinus brucus | native | Bramble shark | Japanese : Kikuzame |
| Echinorhiniformes | Echinorhinidae | Echinorhinus cookei | native | Prickly shark | Japanese : Kogikuzame |
| Ophidiiformes | Carapidae | Echiodon anchipterus | native | Closefin pearlfish | Japanese : Kumano-kakureuo |
| Stomiiformes | Stomiidae | Echiostoma barbatum | native | Threadfin dragonfish | Japanese : Murasaki-hoshi-eso |
| Blenniiformes | Blenniidae | Ecsenius bicolor | native | Bicolor blenny | Japanese : Futairokaeru-uo |
| Blenniiformes | Blenniidae | Ecsenius lineatus | native | Linear blenny | Japanese : Hitosujiginpo |
| Blenniiformes | Blenniidae | Ecsenius midas | native | Persian blenny | |
| Blenniiformes | Blenniidae | Ecsenius namiyei | native | Black comb-tooth | |
| Blenniiformes | Blenniidae | Ecsenius oculus | native | Ocular blenny | Japanese : Goishiginpo |
| Blenniiformes | Blenniidae | Ecsenius yaeyamaensis | native | Yaeyama blenny | Japanese : Ishigaki-kaeru-uo |
| Perciformes/Scorpaenoidei | Setarchidae | Ectreposebastes imus | native | Midwater scorpionfish | Japanese : Kurokasago |
| Carangiformes | Carangidae | Elagatis bipinnulata | native | Rainbow runner | Japanese : Tsumuburi |
| Perciformes/Cottoidei | Liparidae | Elassodiscus tremebundus | native | ||
| Myctophiformes | Myctophidae | Electrona risso | native | Electric lantern fish | Japanese : Tsumari- darumahadaka |
| Gadiformes | Gadidae | Eleginus gracilis | native | Saffron cod | Japanese : Komai |
| Gobiiformes | Eleotridae | Eleotris acanthopomus | native | Spinecheek gudgeon | Japanese : Chichibumodoki |
| Gobiiformes | Eleotridae | Eleotris fusca | native | Dusky sleeper | Japanese : Tenjiku-kawa-anago |
| Gobiiformes | Eleotridae | Eleotris melanosoma | native | Broadhead sleeper | Japanese : Okamehaze |
| Gobiiformes | Eleotridae | Eleotris oxycephala | native | Japanese : Kawa-anago | |
| Callionymiformes | Callionymidae | Eleutherochir opercularis | native | Flap-gilled dragonet | Japanese : Ôkuchi-numeri |
| Carangaria/misc | Polynemidae | Eleutheronema rhadinum | native | East Asian fourfinger threadfin | Japanese : Minami-konoshiro |
| Mugiliformes | Mugilidae | Ellochelon vaigiensis | native | Squaretail mullet | Japanese : Oni-bora |
| Elopiformes | Elopidae | Elops hawaiensis | native | Hawaiian ladyfish | Japanese : Kara-iwashi |
| Elopiformes | Elopidae | Elops machnata | native | Tenpounder | |
| Eupercaria/misc | Emmelichthyidae | Emmelichthys struhsakeri | native | Golden redbait | Japanese : Rôsoku-chibiki |
| Ophidiiformes | Carapidae | Encheliophis boraborensis | native | Pinhead pearlfish | Japanese : Bôzu-kakureuo |
| Ophidiiformes | Carapidae | Encheliophis gracilis | native | Graceful pearlfish | Japanese : Shimofuri-kakureuo |
| Ophidiiformes | Carapidae | Encheliophis homei | native | Silver pearlfish | Japanese : Tenaga-kakureuo |
| Ophidiiformes | Carapidae | Encheliophis sagamianus | native | Japanese : Kakureuo | |
| Ophidiiformes | Carapidae | Encheliophis vermicularis | native | Worm pearlfish | Japanese : Amamai-kakureuo |
| Anguilliformes | Muraenidae | Enchelycore lichenosa | native | Reticulate hookjaw moray | Japanese : Koke-utsubo |
| Anguilliformes | Muraenidae | Enchelycore pardalis | native | Leopard moray eel | Japanese : Tora-utsubo |
| Anguilliformes | Muraenidae | Enchelycore schismatorhynchus | native | White-margined moray | Japanese : Hida-utsubo |
| Anguilliformes | Muraenidae | Enchelynassa canina | native | Longfang moray | |
| Blenniiformes | Blenniidae | Enchelyurus kraussii | native | Krauss' blenny | Japanese : Kuroginpo |
| Clupeiformes | Engraulidae | Encrasicholina heteroloba | native | Shorthead anchovy | Japanese : Mizusururu |
| Clupeiformes | Engraulidae | Encrasicholina punctifer | native | Buccaneer anchovy | Japanese : Taiyo tarekuchi |
| Clupeiformes | Engraulidae | Engraulis japonicus | native | Japanese anchovy | Japanese : Katakuchi-iwashi |
| Pleuronectiformes | Bothidae | Engyprosopon grandisquama | native | Largescale flounder | Japanese : Darumagarei |
| Pleuronectiformes | Bothidae | Engyprosopon kushimotoense | native | Japanese : Kushimoto-darumagarei | |
| Pleuronectiformes | Bothidae | Engyprosopon longipelvis | native | Japanese : Hime-darumagarei | |
| Pleuronectiformes | Bothidae | Engyprosopon maldivense | native | Olive wide-eyed flounder | Japanese : Tenaga-darumagarei |
| Pleuronectiformes | Bothidae | Engyprosopon multisquama | native | Japanese : Chikame-darumagarei | |
| Pleuronectiformes | Bothidae | Engyprosopon xystrias | native | Japanese : Nise-darumagarei | |
| Blenniiformes | Tripterygiidae | Enneapterygius bahasa | native | Blacktail threefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius elegans | native | Hourglass triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius etheostoma | native | Japanese : Hebiginpo | |
| Blenniiformes | Tripterygiidae | Enneapterygius flavoccipitis | native | Yellownape tripplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius hemimelas | native | Halfblack Triplefin | Japanese : Gomafu-hebiginpo |
| Blenniiformes | Tripterygiidae | Enneapterygius leucopunctatus | native | White spotted triplefin | Japanese : Hakuten-hebigimpo |
| Blenniiformes | Tripterygiidae | Enneapterygius miyakensis | native | Izu Islands triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius nigricauda | native | Blacktail triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius pallidoserialis | native | Pale white-spotted triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius philippinus | native | Minute triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius phoenicosoma | native | Red-bodied triplefin | Japanese : Aka-hebigimpo |
| Blenniiformes | Tripterygiidae | Enneapterygius rubicauda | native | Redtail triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius senoui | native | Japanese : Kibire-hebiginpo | |
| Blenniiformes | Tripterygiidae | Enneapterygius sericus | native | Spotted-head triplefin | Japanese : Tenten-hebigimpo |
| Blenniiformes | Tripterygiidae | Enneapterygius signicauda | native | Flagtail triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius similis | native | Black-and-Red Triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius tutuilae | native | High-hat Triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius unimaculatus | native | Onespot triplefin | |
| Blenniiformes | Tripterygiidae | Enneapterygius vexillarius | native | Blacksaddle triplefin | |
| Perciformes/Cottoidei | Cottidae | Enophrys diceraus | native | Antlered sculpin | Japanese : Onikajika |
| Blenniiformes | Blenniidae | Entomacrodus caudofasciatus | native | Tail-barred rockskipper | Japanese : Aomonginpo |
| Blenniiformes | Blenniidae | Entomacrodus decussatus | native | Wavy-lined blenny | Japanese : Kikai-kaeru-uo |
| Blenniiformes | Blenniidae | Entomacrodus niuafoouensis | native | Tattoo-chin rockskipper | Japanese : Keshôginpo |
| Blenniiformes | Blenniidae | Entomacrodus sealei | native | Seale's rockskipper | |
| Blenniiformes | Blenniidae | Entomacrodus stellifer | native | Stellar rockskipper | Japanese : Hoshi-ginpo |
| Blenniiformes | Blenniidae | Entomacrodus striatus | native | Reef margin blenny | Japanese : Sujiginpo |
| Blenniiformes | Blenniidae | Entomacrodus thalassinus | native | Sea blenny | Japanese : Goten-kaeru-uo |
| Petromyzontiformes | Petromyzontidae | Entosphenus tridentatus | native | Pacific lamprey | Japanese : Mitsuba-yatsume |
| Pleuronectiformes | Pleuronectidae | Eopsetta grigorjewi | native | Shotted halibut | Japanese : Mushigarei |
| Acanthuriformes | Ephippidae | Ephippus orbis | native | Orbfish | Japanese : Manjûdai |
| Eupercaria/misc | Labridae | Epibulus insidiator | native | Sling-jaw wrasse | Japanese : Gichibera |
| Acropomatiformes | Epigonidae | Epigonus atherinoides | native | Japanese : Hira-yasemutsu | |
| Acropomatiformes | Epigonidae | Epigonus ctenolepis | native | Japanese : Naga-yasemutsu | |
| Acropomatiformes | Epigonidae | Epigonus denticulatus | native | Pencil cardinal | Japanese : Hage-yasemutsu |
| Acropomatiformes | Epigonidae | Epigonus pectinifer | native | Japanese : Yasemutsu | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus akaara | native | Hong Kong grouper | Japanese : Kijihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus amblycephalus | native | Banded grouper | Japanese : Kokuten-aohata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus areolatus | native | Areolate grouper | Japanese : Omon-hata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus awoara | native | Yellow grouper | Japanese : Aohata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus bleekeri | native | Duskytail grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus bruneus | native | Longtooth grouper | Japanese : Kue |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus coeruleopunctatus | native | Whitespotted grouper | Japanese : Hakuten-hata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus coioides | native | Orange-spotted grouper | Japanese : Chairomaruhata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus cyanopodus | native | Speckled blue grouper | Japanese : Tsuchihozeri |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus epistictus | native | Dotted grouper | Japanese : Komon-hata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus fasciatomaculosus | native | Rock grouper | Japanese : Obihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus fasciatus | native | Blacktip grouper | Japanese : Akahata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus fuscoguttatus | native | Brown-marbled grouper | Japanese : Aka-madarahata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus hexagonatus | native | Starspotted grouper | Japanese : Ishigakihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus howlandi | native | Blacksaddle grouper | Japanese : Hiregurohata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus insularis | native | Pacifc insular grouper; | Japanese : Mahoroba-hata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus irroratus | native | Marquesan grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus japonicus | native | Japanese : Hôsekihata | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus kupangensis | native | Fivebar grouper | Japanese : Kokuten-aohata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus lanceolatus | native | Giant grouper | Japanese : Tamakai |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus latifasciatus | native | Striped grouper | Japanese : Osujihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus macrospilos | native | Snubnose grouper | Japanese : Kibirehata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus maculatus | native | Highfin grouper | Japanese : Shirobuchihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus malabaricus | native | Malabar grouper | Japanese : Chairomaruhata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus melanostigma | native | One-blotch grouper | Japanese : Sumitsukihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus merra | native | Honeycomb grouper | Japanese : Kaumonhata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus miliaris | native | Netfin grouper | Japanese : Hoosekihata-modoki |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus morrhua | native | Comet grouper | Japanese : Hôkihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus ongus | native | White-streaked grouper | Japanese : Namihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus poecilonotus | native | Dot-dash grouper | Japanese : Iyagohata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus polyphekadion | native | Camouflage grouper | Japanese : Madarahata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus quoyanus | native | Longfin grouper | Japanese : Mayôhata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus radiatus | native | Oblique-banded grouper | Japanese : Kakehashihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus retouti | native | Red-tipped grouper | Japanese : Akahata-modoki |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus rivulatus | native | Halfmoon grouper | Japanese : Shimofurihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus socialis | native | Surge grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus stictus | native | Black-dotted grouper | Japanese : Aohata-modoki |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus suborbitalis | native | Seamount grouper | |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus tauvina | native | Greasy grouper | Japanese : Hitomihata |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus trimaculatus | native | Threespot grouper | Japanese : Nominokuchi |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus tukula | native | Potato grouper | Japanese : Kasurihata |
| Scombriformes | Gempylidae | Epinnula rex | native | Pacific Domine | |
| Myxiniformes | Myxinidae | Eptatretus atami | native | Brown hagfish | Japanese : Kuro-mekura-unagi |
| Myxiniformes | Myxinidae | Eptatretus burgeri | native | Inshore hagfish | Japanese : Nuta-unagi |
| Myxiniformes | Myxinidae | Eptatretus moki | native | ||
| Myxiniformes | Myxinidae | Eptatretus okinoseanus | native | Japanese : Murasaki-nuta-unagi | |
| Myxiniformes | Myxinidae | Eptatretus walkeri | native | ||
| Acanthuriformes | Leiognathidae | Equulites berbis | native | Berber ponyfish | Japanese : Itohiki-hiiragi |
| Acanthuriformes | Leiognathidae | Equulites leuciscus | native | Whipfin ponyfish | Japanese : Itohiki-hiiragi |
| Acanthuriformes | Leiognathidae | Equulites lineolatus | native | Ornate ponyfish | Japanese : Ito-hiiragi |
| Acanthuriformes | Leiognathidae | Equulites popei | native | Pope's ponyfish | Japanese : Hime-hiiragi |
| Acanthuriformes | Leiognathidae | Equulites rivulatus | native | Japanese : Oki-hiiragi | |
| Acanthuriformes | Leiognathidae | Equulites ryukyuensis | native | Okinawan whip-fin ponyfish | Japanese : Okinawa-itohiki-hiiragi |
| Ophidiiformes | Ophidiidae | Eretmichthys pinnatus | native | Japanese : Furisode-ashiro | |
| Perciformes/Cottoidei | Rhamphocottidae | Ereunias grallator | native | Japanese : Torikajika | |
| Perciformes/Zoarcoidei | Zoarcidae | Ericandersonia sagamia | native | Japanese : Suzakugenge | |
| Perciformes/Cottoidei | Anoplopomatidae | Erilepis zonifer | native | Skilfish | Japanese : Aburabôzu |
| Perciformes/Scorpaenoidei | Aploactinidae | Erisphex pottii | native | Japanese : Abu-okoze | |
| Perciformes/Zoarcoidei | Stichaeidae | Ernogrammus hexagrammus | native | Six-lined prickleback | Japanese : Musujigaji |
| Perciformes/Scorpaenoidei | Synanceiidae | Erosa erosa | native | Pitted stonefish | Japanese : Darumaokoze |
| Eupercaria/misc | Emmelichthyidae | Erythrocles microceps | native | Japanese : Hi-chibiki | |
| Eupercaria/misc | Emmelichthyidae | Erythrocles schlegelii | native | Japanese rubyfish | Japanese : Hachibiki |
| Eupercaria/misc | Emmelichthyidae | Erythrocles scintillans | native | Golden kali kali | Japanese : Hawai-chibiki |
| Eupercaria/misc | Lutjanidae | Etelis carbunculus | native | Deep-water red snapper | Japanese : Hachijô-akamutsu |
| Eupercaria/misc | Lutjanidae | Etelis coruscans | native | Deepwater longtail red snapper | Japanese : Hamadai |
| Eupercaria/misc | Lutjanidae | Etelis radiosus | native | Pale snapper | Japanese : Ôkuchi-hamadai |
| Squaliformes | Etmopteridae | Etmopterus brachyurus | native | Shorttail lanternshark | |
| Squaliformes | Etmopteridae | Etmopterus lucifer | native | Blackbelly lanternshark | Japanese : Fujikujira |
| Squaliformes | Etmopteridae | Etmopterus pusillus | native | Smooth lanternshark | Japanese : Karasuzame |
| Squaliformes | Etmopteridae | Etmopterus sheikoi | endemic | Rasptooth dogfish | |
| Squaliformes | Etmopteridae | Etmopterus splendidus | native | Splendid lanternshark | Japanese : Futoshimi-fujikujra |
| Squaliformes | Etmopteridae | Etmopterus unicolor | native | Bristled lanternshark | Japanese : Nise-karasuzame |
| Clupeiformes | Dussumieriidae | Etrumeus micropus | native | ||
| Acanthuriformes | Leiognathidae | Eubleekeria splendens | native | Splendid ponyfish | Japanese : Taiwan-hiiragi |
| Beloniformes | Hemiramphidae | Euleptorhamphus viridis | native | Ribbon halfbeak | Japanese : Tô-zayori |
| Perciformes/Zoarcoidei | Eulophiidae | Eulophias spinosior | native | Japanese : Toge-itoginpo | |
| Perciformes/Zoarcoidei | Eulophiidae | Eulophias tanneri | native | Japanese : Itoginpo; Japanese : Owashi-itoginpo; | |
| Lampriformes | Lophotidae | Eumecichthys fiski | native | Unicorn crestfish | Japanese : Tengunotachi |
| Scombriformes | Bramidae | Eumegistus illustris | native | Brilliant pomfret | Japanese : Chikame-echiopia |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus asperrimus | native | Japanese : Konpeitô | |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus awae | native | Japanese : Dango-uo | |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus barbatus | native | Japanese : Hige-dango | |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus lindbergi | native | Japanese : Name-fûsen-uo | |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus orbis | native | Pacific spiny lumpsucker | Japanese : Ibo-dango |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus pacificus | native | Japanese : Fûsen-uo | |
| Perciformes/Cottoidei | Cyclopteridae | Eumicrotremus uenoi | native | Japanese : Sakura-dango-uo | |
| Perciformes/Cottoidei | Psychrolutidae | Eurymen gyrinus | native | Smoothcheek sculpin | Japanese : Yagishirikajika |
| Dactylopteriformes | Pegasidae | Eurypegasus draconis | native | Short dragonfish | Japanese : Umitengu |
| Saccopharyngiformes | Eurypharyngidae | Eurypharynx pelecanoides | native | Pelican eel | Japanese : Fukuro-unagi |
| Ophidiiformes | Carapidae | Eurypleuron owasianum | native | Eel pearlfish | Japanese : Soko-kakureuo |
| Stomiiformes | Stomiidae | Eustomias appositus | native | ||
| Stomiiformes | Stomiidae | Eustomias bifilis | native | Twinthread dragonfish | Japanese : Hosohige-hoshi-eso |
| Stomiiformes | Stomiidae | Eustomias bulbornatus | native | Grapevine dragonfish | Japanese : Kazari-hoshi-eso |
| Stomiiformes | Stomiidae | Eustomias gibbsi | native | ||
| Stomiiformes | Stomiidae | Eustomias interruptus | native | ||
| Stomiiformes | Stomiidae | Eustomias ioani | native | Japanese : Rôsoku-hoshi-eso | |
| Stomiiformes | Stomiidae | Eustomias macrurus | native | Yellowstem dragonfish | Japanese : Inu-hoshi-eso |
| Stomiiformes | Stomiidae | Eustomias monoclonus | native | ||
| Stomiiformes | Stomiidae | Eustomias orientalis | native | Japanese : Dainichi-hoshi-eso | |
| Stomiiformes | Stomiidae | Eustomias schmidti | native | Schmidt's dragonfish | Japanese : Hyôtan-hoshi-eso |
| Gobiiformes | Gobiidae | Eutaeniichthys gilli | native | Japanese : Himohaze | |
| Scombriformes | Scombridae | Euthynnus affinis | native | Kawakawa | Japanese : Suma |
| Aulopiformes | Evermannellidae | Evermannella indica | native | Indian sabretooth | Japanese : Madara-yari-eso |
| Gobiiformes | Gobiidae | Eviota abax | endemic | Sand-table dwarfgoby | Japanese : Isohaze |
| Gobiiformes | Gobiidae | Eviota afelei | native | Afele's dwarfgoby | Japanese : Shima-midorihaze |
| Gobiiformes | Gobiidae | Eviota amamiko | native | Amamiko dwarfgoby | Japanese : Amamiko-isohaze |
| Gobiiformes | Gobiidae | Eviota ancora | native | Hookcheek dwarfgoby | Japanese : Bonbori-Isohaze |
| Gobiiformes | Gobiidae | Eviota atriventris | native | Blackbelly dwarfgoby | Japanese : Shiroobi isohase |
| Gobiiformes | Gobiidae | Eviota bifasciata | native | Twostripe dwarfgoby | Japanese : Oyogi-isohaze |
| Gobiiformes | Gobiidae | Eviota distigma | native | Twospot dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota fallax | native | Twin Dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota fasciola | native | Barred dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota filamentosa | native | Threadfin dwarfgoby | Japanese : Itohiki-Isohaze |
| Gobiiformes | Gobiidae | Eviota flavipinnata | native | Yellowfin dwarfgoby | Japanese : Kibire-isohaze |
| Gobiiformes | Gobiidae | Eviota flebilis | native | Tearful dwarfgoby | Japanese : Shizuki-Isohaze |
| Gobiiformes | Gobiidae | Eviota infulata | native | Shouldermark dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota japonica | native | Japanese dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota korechika | native | Korechika's dwarfoby | Japanese : Shibori-isohaze |
| Gobiiformes | Gobiidae | Eviota lachdeberei | native | Lachdebere's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota lacrimae | native | Teared dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota maculosa | native | Polkadot dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota masudai | native | Masuda's dwarfgoby | Japanese : Aka-isohaze |
| Gobiiformes | Gobiidae | Eviota melasma | native | Headspot dwarfgoby | Japanese : Akahoshi-isohaze |
| Gobiiformes | Gobiidae | Eviota nebulosa | native | Nebulous dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota nigramembrana | native | Blackbar dwarfgoby | Japanese : Kometubu-isohaze |
| Gobiiformes | Gobiidae | Eviota nigrispina | native | Blackspine dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota occasa | native | Sunset dwarfgoby | Japanese : Kijimunaa-isohaze |
| Gobiiformes | Gobiidae | Eviota ocellifer | native | Ocellated dwarfgoby | Japanese : Urauchi-isohaze |
| Gobiiformes | Gobiidae | Eviota pellucida | native | Transparent dwarfgoby | Japanese : Kojika isohaze |
| Gobiiformes | Gobiidae | Eviota perspicilla | native | Glasses dwarfgoby | Japanese : Hoderi-isohaze |
| Gobiiformes | Gobiidae | Eviota prasina | native | Greenbubble dwarfgoby | Japanese : Nanyô-midorihaze |
| Gobiiformes | Gobiidae | Eviota prasites | native | Hairfin dwarfgoby | Japanese : Ao-isohaze |
| Gobiiformes | Gobiidae | Eviota punyit | native | Punyit dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota queenslandica | native | Queensland dwarfgoby | Japanese : Hoshihire-isohaze |
| Gobiiformes | Gobiidae | Eviota rubriguttata | native | Redspotfin dwarfgoby | Japanese : Hanabi-Isohaze |
| Gobiiformes | Gobiidae | Eviota rubrimaculata | native | Redspot dwarfgoby | Japanese : Zakuro-Isohaze |
| Gobiiformes | Gobiidae | Eviota shibukawai | native | Shibukawa's dwarfgoby | Japanese : Akabana-Isohaze |
| Gobiiformes | Gobiidae | Eviota shimadai | native | Shimadai's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota sigillata | native | Adorned dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota smaragdus | native | Emerald dwarfgoby | Japanese : Kurohoshi-isohaze |
| Gobiiformes | Gobiidae | Eviota specca | native | Dusted dwarfgoby | Japanese : Kumadori-Isohaze |
| Gobiiformes | Gobiidae | Eviota storthynx | native | Storthynx dwarfgoby | Japanese : Kinhoshi-isohaze |
| Gobiiformes | Gobiidae | Eviota teresae | native | Terry's dwarfgoby | |
| Gobiiformes | Gobiidae | Eviota toshiyuki | native | Toshiyuki's dwarfgoby | Japanese : Midorihaze |
| Gobiiformes | Gobiidae | Eviota zonura | native | Zoned dwarfgoby | |
| Acropomatiformes | Pentacerotidae | Evistias acutirostris | native | Striped boarfish | Japanese : Tengudai |
| Scombriformes | Trichiuridae | Evoxymetopon macrophthalmus | native | Bigeye scabbard fish | Japanese : Hirenaga-oome-yumetachi |
| Scombriformes | Trichiuridae | Evoxymetopon poeyi | native | Poey's scabbardfish | Japanese : Hirenaga-yumetachi |
| Scombriformes | Trichiuridae | Evoxymetopon taeniatum | native | Channel scabbardfish | Japanese : Yumetachimodoki |
| Eupercaria/misc | Sparidae | Evynnis cardinalis | native | Threadfin porgy | Japanese : Hirekodai |
| Eupercaria/misc | Sparidae | Evynnis tumifrons | native | Yellowback seabream | Japanese : Chidai; Japanese : Ki-dai; |
| Blenniiformes | Blenniidae | Exallias brevis | native | Leopard blenny | Japanese : Sedakaginpo |
| Beloniformes | Exocoetidae | Exocoetus monocirrhus | native | Barbel flyingfish | Japanese : Hagoromo-tobi-uo |
| Beloniformes | Exocoetidae | Exocoetus volitans | native | Tropical two-wing flyingfish | Japanese : Idaten-tobi-uo |
| Gobiiformes | Gobiidae | Exyrias akihito | native | Akihito's goby | |
| Gobiiformes | Gobiidae | Exyrias belissimus | native | Mud reef-goby | Japanese : Obake-inkohaze |
| Gobiiformes | Gobiidae | Exyrias puntang | native | Puntang goby | Japanese : Inkohaze |
| Gobiiformes | Gobiidae | Favonigobius gymnauchen | native | Sharp-nosed sand goby | Japanese : Himehaze |
| Gobiiformes | Gobiidae | Favonigobius melanobranchus | native | Blackthroat goby | |
| Gobiiformes | Gobiidae | Favonigobius reichei | native | Indo-Pacific tropical sand goby | Japanese : Minami-himehaze |
| Gobiiformes | Gobiidae | Feia nympha | native | Nymph goby | |
| Carangiformes | Carangidae | Ferdauia ferdau | native | Blue trevally | Japanese : Kurohira-aji |
| Carangiformes | Carangidae | Ferdauia orthogrammus | native | Island trevally | Japanese : Nanyô-kaiwari |
| Syngnathiformes | Syngnathidae | Festucalex erythraeus | native | Japanese : Amakusayôji | |
| Kurtiformes | Apogonidae | Fibramia amboinensis | native | Amboina cardinalfish | Japanese : Amami ishimochi |
| Kurtiformes | Apogonidae | Fibramia lateralis | native | Humpback cardinal | |
| Kurtiformes | Apogonidae | Fibramia thermalis | native | Half-barred cardinal | Japanese : Sangiru-ishimochi |
| Syngnathiformes | Fistulariidae | Fistularia commersonii | native | Bluespotted cornetfish | Japanese : Aka-yagara |
| Syngnathiformes | Fistulariidae | Fistularia petimba | native | Red cornetfish | Japanese : Ao-yagara |
| Gobiesociformes | Gobiesocidae | Flabellicauda akiko | native | ||
| Stomiiformes | Stomiidae | Flagellostomias boureei | native | Longbarb dragonfish | Japanese : Muchi-hoshi-eso |
| Carangiformes | Carangidae | Flavocaranx bajad | native | Orangespotted trevally | Japanese : Kogane-aji |
| Kurtiformes | Apogonidae | Foa fo | native | Weedy cardinalfish | |
| Callionymiformes | Callionymidae | Foetorepus kamoharai | native | Japanese : Amime-nodokusari | |
| Callionymiformes | Callionymidae | Foetorepus masudai | native | Masuda's dragonet | Japanese : Ruson-beni-teguri |
| Acanthuriformes | Chaetodontidae | Forcipiger flavissimus | native | Forcepsfish | Japanese : Fueyakkodai |
| Acanthuriformes | Chaetodontidae | Forcipiger longirostris | native | Longnose butterflyfish | Japanese : Ôfueyakkodai |
| Kurtiformes | Apogonidae | Fowleria aurita | native | Crosseyed cardinalfish | |
| Kurtiformes | Apogonidae | Fowleria isostigma | native | Dotted cardinalfish | Japanese : Naha-mato-ishimochi |
| Kurtiformes | Apogonidae | Fowleria marmorata | native | Marbled cardinalfish | Japanese : Obi-shibori |
| Kurtiformes | Apogonidae | Fowleria punctulata | native | Spotcheek cardinalfish | Japanese : Nahamato-ishimochi |
| Kurtiformes | Apogonidae | Fowleria vaiulae | native | Mottled cardinalfish | Japanese : Shibori-damashi |
| Kurtiformes | Apogonidae | Fowleria variegata | native | Variegated cardinalfish | Japanese : Shibori |
| Lophiiformes | Antennariidae | Fowlerichthys scriptissimus | native | Japanese : Sarasa-izariuo; Japanese : Sōshi-izariuo; | |
| Perciformes/Cottoidei | Agonidae | Freemanichthys thompsoni | native | Japanese : Yase-tokubire | |
| Perciformes/Cottoidei | Cottidae | Furcina ishikawae | native | Ishikawa's sculpin | Japanese : Sarasakajika |
| Perciformes/Cottoidei | Cottidae | Furcina osimae | native | Japanese : Kinukajika | |
| Gobiiformes | Gobiidae | Fusigobius duospilus | native | Barenape goby | |
| Gobiiformes | Gobiidae | Fusigobius gracilis | native | Slender sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius humeralis | native | Shoulderspot sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius inframaculatus | native | Innerspotted sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius longispinus | native | Orange-spotted sand-goby | Japanese : Hatatate-sankakuhaze |
| Gobiiformes | Gobiidae | Fusigobius maximus | native | Large sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius melacron | native | Blacktip sandgoby | |
| Gobiiformes | Gobiidae | Fusigobius neophytus | native | Common fusegoby | Japanese : Sankakuhaze |
| Gobiiformes | Gobiidae | Fusigobius signipinnis | native | Signalfin goby | Japanese : Hirefuri sankaku haze |
| Gadiformes | Moridae | Gadella jordani | native | Jordan's cod | Japanese : Naga-chigodara |
| Gadiformes | Bathygadidae | Gadomus colletti | native | Japanese : Katadara | |
| Gadiformes | Bathygadidae | Gadomus multifilis | native | Japanese : Nodoguro-katadara | |
| Gadiformes | Gadidae | Gadus chalcogrammus | native | Alaska pollock | Japanese : Suketôdara |
| Gadiformes | Gadidae | Gadus macrocephalus | native | Pacific cod | Japanese : Madara |
| Carcharhiniformes | Galeocerdonidae | Galeocerdo cuvier | native | Tiger shark | Japanese : Itachizame |
| Carcharhiniformes | Pentanchidae | Galeus eastmani | native | Gecko catshark | Japanese : Yamorizame |
| Carcharhiniformes | Pentanchidae | Galeus longirostris | native | Longnose sawtail cat shark | Japanese : Hashinaga-yamorizame |
| Carcharhiniformes | Pentanchidae | Galeus nipponensis | native | Broadfin sawtail catshark | Japanese : Nihon-yamorizame |
| Carcharhiniformes | Pentanchidae | Galeus sauteri | native | Blacktip sawtail catshark | Japanese : Taiwan-yamorizame |
| Cyprinodontiformes | Poeciliidae | Gambusia affinis | introduced | Mosquitofish | Japanese : Kadayashi |
| Perciformes/Scorpaenoidei | Peristediidae | Gargariscus prionocephalus | native | Jaggedhead gurnard | Japanese : Onikihôbô |
| Perciformes/Gasterosteoidei | Gasterosteidae | Gasterosteus aculeatus | native | Three-spined stickleback | Japanese : Hariyo |
| Perciformes/Gasterosteoidei | Gasterosteidae | Gasterosteus microcephalus | native | Japanese : Hariyo | |
| Perciformes/Gasterosteoidei | Gasterosteidae | Gasterosteus nipponicus | native | ||
| Anguilliformes | Muraenesocidae | Gavialiceps taiwanensis | native | ||
| Acanthuriformes | Leiognathidae | Gazza minuta | native | Toothpony | Japanese : Koban-hiiragi |
| Acanthuriformes | Leiognathidae | Gazza rhombea | native | Rhomboid toothpony | Japanese : Hishi-koban-hiiragi |
| Scombriformes | Gempylidae | Gempylus serpens | native | Snake mackerel | Japanese : Kurotachikamasu |
| Acanthuriformes | Pomacanthidae | Genicanthus lamarck | native | Blackstriped angelfish | Japanese : Tatejimayakko |
| Acanthuriformes | Pomacanthidae | Genicanthus melanospilos | native | Spotbreast angelfish | Japanese : Yaitoyakko |
| Acanthuriformes | Pomacanthidae | Genicanthus semifasciatus | native | Japanese swallow | Japanese : Tosayakko |
| Acanthuriformes | Pomacanthidae | Genicanthus takeuchii | native | Spotted angelfish | Japanese : Mizutama-yakko |
| Acanthuriformes | Pomacanthidae | Genicanthus watanabei | native | Blackedged angelfish | Japanese : Hirenagayakko |
| Trachichthyiformes | Trachichthyidae | Gephyroberyx japonicus | native | Big roughy | Japanese : Hashikinme |
| Eupercaria/misc | Gerreidae | Gerres akazakii | endemic | Japanese tenspined silver-biddy | Japanese : Sedaka-daimyosagi |
| Eupercaria/misc | Gerreidae | Gerres baconensis | native | Scaly snouted silver-biddy | Japanese : Ogasawara-kurosagi |
| Eupercaria/misc | Gerreidae | Gerres equulus | native | Japanese : Kurosagi | |
| Eupercaria/misc | Gerreidae | Gerres erythrourus | native | Deepbody mojarra | Japanese : Sepparisagi |
| Eupercaria/misc | Gerreidae | Gerres filamentosus | native | Whipfin silverbiddy | Japanese : Itohikisagi |
| Eupercaria/misc | Gerreidae | Gerres japonicus | native | Japanese silver-biddy | Japanese : Daimyôsagi |
| Eupercaria/misc | Gerreidae | Gerres longirostris | native | Strongspine silver-biddy | Japanese : Tsupparisagi |
| Eupercaria/misc | Gerreidae | Gerres macracanthus | native | Longspine silverbiddy | Japanese : Hosoitohiki-sagi |
| Eupercaria/misc | Gerreidae | Gerres microphthalmus | native | Small-eyed whipfin mojarra | Japanese : Yamato-itohikisagi |
| Eupercaria/misc | Gerreidae | Gerres oblongus | native | Slender silverbiddy | Japanese : Nagasagi |
| Eupercaria/misc | Gerreidae | Gerres oyena | native | Common silverbiddy | Japanese : Minami-kurosagi |
| Eupercaria/misc | Gerreidae | Gerres ryukyuensis | native | Ryukyu banded silver-biddy | Japanese : Yanbaru-sagi |
| Eupercaria/misc | Gerreidae | Gerres shima | native | Banded silver-biddy | Japanese : Shima-kurosagi |
| Lophiiformes | Gigantactinidae | Gigantactis balushkini | native | ||
| Lophiiformes | Gigantactinidae | Gigantactis elsmani | native | Japanese : Rôsoku-mogura-ankô | |
| Lophiiformes | Gigantactinidae | Gigantactis gargantua | native | Japanese : Onaga-mogura-ankô | |
| Lophiiformes | Gigantactinidae | Gigantactis kreffti | native | Japanese : Kurefuto-ankô | |
| Lophiiformes | Gigantactinidae | Gigantactis perlatus | native | Japanese : Andon-mogura-ankô | |
| Lophiiformes | Gigantactinidae | Gigantactis vanhoeffeni | native | Japanese : Shida-ankô | |
| Perciformes/Serranoidei | Anthiadidae | Giganthias immaculatus | native | Japanese : Mihara-hanadai | |
| Perciformes/Cottoidei | Psychrolutidae | Gilbertidia pustulosa | native | ||
| Centrarchiformes | Girellidae | Girella leonina | native | Japanese : Kuromejina | |
| Centrarchiformes | Girellidae | Girella mezina | native | Japanese : Okina-mejina | |
| Centrarchiformes | Girellidae | Girella punctata | native | Largescale blackfish | Japanese : Mejina |
| Gobiiformes | Gobiidae | Gladiogobius ensifer | native | Gladiator goby | Japanese : Togenagahaze |
| Acropomatiformes | Glaucosomatidae | Glaucosoma buergeri | native | Deepsea jewfish | Japanese : Aobadai |
| Acropomatiformes | Glaucosomatidae | Glaucosoma hebraicum | native | West Australian dhufish | Japanese : Aobadai |
| Rhinopristiformes | Glaucostegidae | Glaucostegus thouin | native | Thouin ray | |
| Argentiniformes | Argentinidae | Glossanodon kotakamaru | native | Kotaka's argentine | Japanese : Kotaka-nigisu |
| Argentiniformes | Argentinidae | Glossanodon lineatus | native | Japanese : Ichimonji-iwashi | |
| Argentiniformes | Argentinidae | Glossanodon semifasciatus | native | Deep-sea smelt | Japanese : Nigisu |
| Gobiiformes | Gobiidae | Glossogobius aureus | native | Golden tank goby | Japanese : Konjikihaze |
| Gobiiformes | Gobiidae | Glossogobius bicirrhosus | native | Bearded flathead goby | Japanese : Agohigehaze |
| Gobiiformes | Gobiidae | Glossogobius celebius | native | Celebes goby | Japanese : Iwahaze |
| Gobiiformes | Gobiidae | Glossogobius circumspectus | native | Circumspect goby | |
| Gobiiformes | Gobiidae | Glossogobius giuris | native | Tank goby | |
| Gobiiformes | Gobiidae | Glossogobius illimis | native | ||
| Gobiiformes | Gobiidae | Glossogobius olivaceus | native | Japanese : Urohaze | |
| Pleuronectiformes | Pleuronectidae | Glyptocephalus kitaharae | native | Willowy flounder | Japanese : Yanagimushigarei |
| Pleuronectiformes | Pleuronectidae | Glyptocephalus stelleri | native | Blackfin flounder | Japanese : Hireguro |
| Blenniiformes | Blenniidae | Glyptoparus delicatulus | native | Delicate blenny | Japanese : Yaitoginpo |
| Ophidiiformes | Ophidiidae | Glyptophidium japonicum | native | Japanese cusk | |
| Ophidiiformes | Ophidiidae | Glyptophidium oceanium | native | Japanese : Shirochôman | |
| Carangiformes | Carangidae | Gnathanodon speciosus | native | Golden trevally | Japanese : Koganeshima-aji |
| Eupercaria/misc | Lethrinidae | Gnathodentex aureolineatus | native | Striped large-eye bream | Japanese : Nokogiri-dai |
| Gobiiformes | Gobiidae | Gnatholepis anjerensis | native | Eye-bar goby | Japanese : Ade-ômonhaze |
| Gobiiformes | Gobiidae | Gnatholepis cauerensis | native | Eyebar goby | Japanese : Kataboshi-ômonhaze |
| Gobiiformes | Gobiidae | Gnatholepis ophthalmotaenia | native | ||
| Gobiiformes | Gobiidae | Gnatholepis yoshinoi | native | Yoshino's goby | Japanese : Hishihire-oomonhaze |
| Anguilliformes | Congridae | Gnathophis ginanago | native | Japanese : Nise-gin-anago | |
| Anguilliformes | Congridae | Gnathophis heterognathos | native | ||
| Anguilliformes | Congridae | Gnathophis nystromi | native | Japanese : Gin-anago | |
| Anguilliformes | Congridae | Gnathophis xenica | native | Japanese : Hime-gin-anago | |
| Cypriniformes | Gobionidae | Gnathopogon caerulescens | native | Japanese : Honmoroko | |
| Cypriniformes | Gobionidae | Gnathopogon elongatus | native | Japanese : Tamoroko | |
| Gobiiformes | Gobiidae | Gobiodon albofasciatus | native | Whitelined coral goby | Japanese : Ichimonji-kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon aoyagii | native | Japanese : Akaten-koban-haze | |
| Gobiiformes | Gobiidae | Gobiodon atrangulatus | native | Japanese : Seaka-kobanhaze | |
| Gobiiformes | Gobiidae | Gobiodon axillaris | native | Red-striped coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon citrinus | native | Poison goby | Japanese : Kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon erythrospilus | native | Japanese : Shuobi-koban-haze | |
| Gobiiformes | Gobiidae | Gobiodon fulvus | native | ||
| Gobiiformes | Gobiidae | Gobiodon fuscoruber | native | Brown-red coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon histrio | native | Broad-barred goby | |
| Gobiiformes | Gobiidae | Gobiodon micropus | native | Japanese : Ai-kobanhaze | |
| Gobiiformes | Gobiidae | Gobiodon multilineatus | native | Japanese : Tasuji-kobanhaze | |
| Gobiiformes | Gobiidae | Gobiodon oculolineatus | native | Eyeline coralgoby | Japanese : Futasuji-kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon okinawae | native | Okinawa goby | Japanese : Kiiro-sangohaze |
| Gobiiformes | Gobiidae | Gobiodon prolixus | native | Elongate coralgoby | |
| Gobiiformes | Gobiidae | Gobiodon quinquestrigatus | native | Five-lined coral goby | Japanese : Futairo-sangohaze |
| Gobiiformes | Gobiidae | Gobiodon rivulatus | native | Rippled coralgoby | Japanese : Akaten-kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon spadix | native | Akane coral goby | Japanese : Akane-kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon spilophthalmus | native | White-lined coral goby | |
| Gobiiformes | Gobiidae | Gobiodon unicolor | native | Unicolor coralgoby | Japanese : Muji-kobanhaze |
| Gobiiformes | Gobiidae | Gobiodon winterbottomi | native | Japanese : Ohire-kobanhaze | |
| Gobiiformes | Gobiidae | Gobiopsis arenaria | native | Patchwork barbelgoby | Japanese : Isagohaze |
| Gobiiformes | Gobiidae | Gobiopsis liolepis | native | Japanese : Hadarehaze | |
| Gobiiformes | Gobiidae | Gobiopsis namnas | native | Japanese : Bake-isagohaze | |
| Gobiiformes | Gobiidae | Gobiopsis quinquecincta | native | Fiveband barbelgoby | Japanese : Kurakakehaze |
| Gobiiformes | Kraemeriidae | Gobitrichinotus radiocularis | native | Japanese : Naminokohaze | |
| Eupercaria/misc | Labridae | Gomphosus varius | native | Bird wrasse | Japanese : Kugibera |
| Centrarchiformes | Latridae | Goniistius quadricornis | native | Japanese : Yûdachi-takanoha | |
| Centrarchiformes | Latridae | Goniistius zebra | native | Redlip morwong | Japanese : Migimaki |
| Centrarchiformes | Latridae | Goniistius zonatus | native | Spottedtail morwong | Japanese : Takanohadai |
| Gonorynchiformes | Gonorynchidae | Gonorynchus abbreviatus | native | Japanese : Nezumigisu | |
| Gonorynchiformes | Gonorynchidae | Gonorynchus gonorynchus | native | Beaked salmon | |
| Stomiiformes | Gonostomatidae | Gonostoma atlanticum | native | Atlantic fangjaw | Japanese : Tsumari-yoko-eso |
| Anguilliformes | Congridae | Gorgasia japonica | native | Japanese : Shinju-anago | |
| Anguilliformes | Congridae | Gorgasia preclara | native | Splendid garden eel | |
| Anguilliformes | Congridae | Gorgasia taiwanensis | native | ||
| Perciformes/Serranoidei | Epinephelidae | Gracila albomarginata | native | Masked grouper | Japanese : Tatesuji-hata |
| Gobiiformes | Gobiidae | Grallenia arenicola | native | Japanese : Sazare-haze | |
| Pleuronectiformes | Bothidae | Grammatobothus polyophthalmus | native | Threespot flounder | Japanese : Mitsume-darumagarei |
| Eupercaria/misc | Callanthiidae | Grammatonotus macrophthalmus | native | ||
| Eupercaria/misc | Callanthiidae | Grammatonotus surugaensis | native | Japanese : Tenjikuhanadai | |
| Scombriformes | Scombridae | Grammatorcynus bilineatus | native | Doublelined mackerel | Japanese : Nijôsaba |
| Zeiformes | Grammicolepididae | Grammicolepis brachiusculus | native | Thorny tinselfish | Japanese : Ôhishi-matôdai |
| Perciformes/Serranoidei | Grammistidae | Grammistes sexlineatus | native | Goldenstriped soapfish | Japanese : Nunosarashi |
| Perciformes/Serranoidei | Grammistidae | Grammistops ocellatus | native | Ocellate soapfish | Japanese : Janome-nunosarashi |
| Ophidiiformes | Bythitidae | Grammonus robustus | native | Japanese : Semushi-itachiuo | |
| Ophidiiformes | Bythitidae | Grammonus yunokawai | native | ||
| Ateleopodiformes | Ateleopodidae | Guentherus katoi | native | Japanese : Hyomon-shachiburi | |
| Gobiiformes | Microdesmidae | Gunnellichthys curiosus | native | Curious wormfish | |
| Gobiiformes | Microdesmidae | Gunnellichthys monostigma | native | Onespot wormfish | Japanese : Kuroeri-ômewarasubo |
| Gobiiformes | Microdesmidae | Gunnellichthys pleurotaenia | native | Onestripe wormfish | Japanese : Ômewarasubo |
| Gobiiformes | Microdesmidae | Gunnellichthys viridescens | native | Yellowstripe wormfish | |
| Kurtiformes | Apogonidae | Gymnapogon foraminosus | native | ||
| Kurtiformes | Apogonidae | Gymnapogon japonicus | native | Japanese : Kudaribôzugisu | |
| Kurtiformes | Apogonidae | Gymnapogon philippinus | native | Philippine cardinalfish | Japanese : Nanyô-kudaribôzugisu |
| Kurtiformes | Apogonidae | Gymnapogon urospilotus | native | B-spot cardinalfish | Japanese : Komon-kudaribôzugisu |
| Perciformes/Zoarcoidei | Zoarcidae | Gymnelopsis brevifenestrata | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Gymnelopsis ocellata | native | Japanese : Yaitogenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Gymnelopsis ochotensis | native | Japanese : Niramigenge | |
| Perciformes/Cottoidei | Cottidae | Gymnocanthus detrisus | native | Japanese : Sebirokajika | |
| Perciformes/Cottoidei | Cottidae | Gymnocanthus galeatus | native | Armorhead sculpin | Japanese : Chikamekajika |
| Perciformes/Cottoidei | Cottidae | Gymnocanthus herzensteini | native | Japanese : Tsumagurokajika | |
| Perciformes/Cottoidei | Cottidae | Gymnocanthus intermedius | native | Japanese : Aikajika | |
| Perciformes/Cottoidei | Cottidae | Gymnocanthus pistilliger | native | Threaded sculpin | Japanese : Hagekajika |
| Perciformes/Zoarcoidei | Stichaeidae | Gymnoclinus cristulatus | native | Trident prickleback | |
| Eupercaria/misc | Lethrinidae | Gymnocranius elongatus | native | Forktail large-eye bream | Japanese : Onaga-meichidai |
| Eupercaria/misc | Lethrinidae | Gymnocranius euanus | native | Japanese large-eye bream | Japanese : Shirodai |
| Eupercaria/misc | Lethrinidae | Gymnocranius grandoculis | native | Blue-lined large-eye bream | Japanese : Sazanami-dai |
| Eupercaria/misc | Lethrinidae | Gymnocranius griseus | native | Grey large-eye bream | Japanese : Meichi-dai |
| Eupercaria/misc | Lethrinidae | Gymnocranius microdon | native | Blue-spotted large-eye bream | Japanese : Naga-meichi |
| Eupercaria/misc | Lethrinidae | Gymnocranius satoi | native | Blacknape large-eye bream | |
| Gobiiformes | Gobiidae | Gymnogobius breunigii | native | Japanese : Biringo | |
| Gobiiformes | Gobiidae | Gymnogobius castaneus | native | Biringo | Japanese : Biringo |
| Gobiiformes | Gobiidae | Gymnogobius cylindricus | native | Japanese : Kiseruhaze | |
| Gobiiformes | Gobiidae | Gymnogobius heptacanthus | native | Japanese : Nikuhaze | |
| Gobiiformes | Gobiidae | Gymnogobius isaza | endemic | Japanese : Isaza | |
| Gobiiformes | Gobiidae | Gymnogobius macrognathos | native | Japanese : Edohaze | |
| Gobiiformes | Gobiidae | Gymnogobius mororanus | native | Japanese : Hebihaze | |
| Gobiiformes | Gobiidae | Gymnogobius opperiens | native | Japanese : Shima-ukigori | |
| Gobiiformes | Gobiidae | Gymnogobius petschiliensis | native | Japanese : sumi-ukigori | |
| Gobiiformes | Gobiidae | Gymnogobius scrobiculatus | native | Japanese : Kubo-haze | |
| Gobiiformes | Gobiidae | Gymnogobius taranetzi | native | Japanese : Shinjikohaze | |
| Gobiiformes | Gobiidae | Gymnogobius uchidai | native | Japanese : Chikuzen-haze | |
| Gobiiformes | Gobiidae | Gymnogobius urotaenia | native | Japanese : Juzukakehaze; Japanese : Ukigori; | |
| Anguilliformes | Muraenidae | Gymnomuraena zebra | native | Zebra moray | Japanese : Zebura-utsubo |
| Scombriformes | Scombridae | Gymnosarda unicolor | native | Dogtooth tuna | Japanese : Isomaguro |
| Anguilliformes | Muraenidae | Gymnothorax albimarginatus | native | Whitemargin moray | |
| Anguilliformes | Muraenidae | Gymnothorax berndti | native | Y-patterned moray | Japanese : Hawai-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax buroensis | native | Latticetail moray | Japanese : Sango-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax chilospilus | native | Lipspot moray | Japanese : Minami-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax chlamydatus | native | Banded mud moray | |
| Anguilliformes | Muraenidae | Gymnothorax enigmaticus | native | Enigmatic moray | Japanese : Shima-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax eurostus | native | Abbott's moray eel | Japanese : Waka-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax favagineus | native | Laced moray | Japanese : Nisegoishi-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax fimbriatus | native | Fimbriate moray | Japanese : Herigoishi-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax flavimarginatus | native | Yellow-edged moray | Japanese : Goma-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax gracilicauda | native | Slendertail moray | |
| Anguilliformes | Muraenidae | Gymnothorax hepaticus | native | Liver-colored moray eel | |
| Anguilliformes | Muraenidae | Gymnothorax herrei | native | Herre's moray | Japanese : Hanajiro-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax isingteena | native | ||
| Anguilliformes | Muraenidae | Gymnothorax javanicus | native | Giant moray | Japanese : Doku-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax kidako | native | Kidako moray | Japanese : Utsubo |
| Anguilliformes | Muraenidae | Gymnothorax margaritophorus | native | Blotch-necked moray | Japanese : Shinju-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax melatremus | native | Dwarf moray | |
| Anguilliformes | Muraenidae | Gymnothorax meleagris | native | Turkey moray | Japanese : Hanabira-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax minor | native | ||
| Anguilliformes | Muraenidae | Gymnothorax monochrous | native | Drab moray | Japanese : Yami-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax neglectus | native | Japanese : Mizore-utsubo | |
| Anguilliformes | Muraenidae | Gymnothorax nudivomer | native | Yellowmouth moray | Japanese : Ade-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax philippinus | native | Philippines moray | Japanese : Firipin-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax pictus | native | Paintspotted moray | |
| Anguilliformes | Muraenidae | Gymnothorax pindae | native | Pinda moray | Japanese : Nokogiri-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax prionodon | native | Australian mottled moray | Japanese : Yuri-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax pseudothyrsoideus | native | Highfin moray | Japanese : Amime-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax reevesii | native | Reeve's moray | Japanese : Mame-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax reticularis | native | English : Reticulated morey | |
| Anguilliformes | Muraenidae | Gymnothorax richardsonii | native | Richardson's moray | Japanese : Moba-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax rueppelliae | native | Banded moray | Japanese : Kurakake-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax sagmacephalus | native | ||
| Anguilliformes | Muraenidae | Gymnothorax thyrsoideus | native | Greyface moray | Japanese : Sabi-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax undulatus | native | Undulated moray | Japanese : Nami-utsubo |
| Anguilliformes | Muraenidae | Gymnothorax ypsilon | native | Y-bar moray | Japanese : Okinoshima-utsubo |
| Myliobatiformes | Gymnuridae | Gymnura japonica | native | Japanese butterflyray | Japanese : Tsubakuro-ei |
| Myliobatiformes | Gymnuridae | Gymnura poecilura | native | Long-tailed butterfly ray | Japanese : Onaga-tsubakuro-ei |
| Perciformes/Zoarcoidei | Zoarcidae | Hadropogonichthys lindbergi | native | ||
| Carcharhiniformes | Pentanchidae | Halaelurus buergeri | native | Blackspotted catshark | Japanese : Nagasaki-torazame |
| Gadiformes | Moridae | Halargyreus johnsonii | native | Slender codling | Japanese : Karasudara |
| Syngnathiformes | Syngnathidae | Halicampus boothae | native | Booth's pipefish | |
| Syngnathiformes | Syngnathidae | Halicampus brocki | native | Brock's pipefish | |
| Syngnathiformes | Syngnathidae | Halicampus dunckeri | native | Duncker's pipefish | Japanese : Hoso-umiyakko |
| Syngnathiformes | Syngnathidae | Halicampus grayi | native | Gray's pipefish | Japanese : Umiyakko |
| Syngnathiformes | Syngnathidae | Halicampus nitidus | native | Glittering pipefish | |
| Syngnathiformes | Syngnathidae | Halicampus punctatus | endemic | Starry pipefish | Japanese : Hoshiyôji |
| Eupercaria/misc | Labridae | Halichoeres argus | native | Argus wrasse | Japanese : Kumadori-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres biocellatus | native | Red-lined wrasse | Japanese : Nishiki-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres bleekeri | native | Japanese : Honbera | |
| Eupercaria/misc | Labridae | Halichoeres chrysus | native | Canary wrasse | Japanese : Kogane-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres claudia | native | Claudia's wrasse | |
| Eupercaria/misc | Labridae | Halichoeres hartzfeldii | native | Hartzfeld's wrasse | Japanese : Kisuji-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres hortulanus | native | Checkerboard wrasse | Japanese : Tokarabera |
| Eupercaria/misc | Labridae | Halichoeres kneri | native | Kner's wrasse | |
| Eupercaria/misc | Labridae | Halichoeres leucurus | native | Greyhead wrasse | |
| Eupercaria/misc | Labridae | Halichoeres margaritaceus | native | Pink-belly wrasse | Japanese : Akanijibera |
| Eupercaria/misc | Labridae | Halichoeres marginatus | native | Dusky wrasse | Japanese : Kanokobera |
| Eupercaria/misc | Labridae | Halichoeres melanochir | native | Orangefin wrasse | Japanese : Munaten-bera |
| Eupercaria/misc | Labridae | Halichoeres melanurus | native | Tailspot wrasse | Japanese : Kazari-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres melasmapomus | native | Cheekspot wrasse | |
| Eupercaria/misc | Labridae | Halichoeres miniatus | native | Circle-cheek wrasse | Japanese : Hohowa-kyûsen |
| Eupercaria/misc | Labridae | Halichoeres nebulosus | native | Nebulous wrasse | Japanese : Inazumabera |
| Eupercaria/misc | Labridae | Halichoeres nigrescens | native | Bubblefin wrasse | |
| Eupercaria/misc | Labridae | Halichoeres orientalis | native | Japanese : Tsukibera | |
| Eupercaria/misc | Labridae | Halichoeres ornatissimus | native | Ornamented wrasse | |
| Eupercaria/misc | Labridae | Halichoeres prosopeion | native | Twotone wrasse | Japanese : Munatenbera-damashi |
| Eupercaria/misc | Labridae | Halichoeres richmondi | native | Richmond's wrasse | |
| Eupercaria/misc | Labridae | Halichoeres scapularis | native | Zigzag wrasse | Japanese : Seitenbera |
| Eupercaria/misc | Labridae | Halichoeres trimaculatus | native | Threespot wrasse | Japanese : Mitsuboshi-kyusen |
| Eupercaria/misc | Labridae | Halichoeres zeylonicus | native | Goldstripe wrasse | |
| Lophiiformes | Ogcocephalidae | Halicmetus niger | native | ||
| Lophiiformes | Ogcocephalidae | Halicmetus reticulatus | native | Marbled seabat | Japanese : Amime fûryû uo |
| Lophiiformes | Ogcocephalidae | Halicmetus ruber | native | Japanese : aka-fûryû-uo | |
| Lophiiformes | Ogcocephalidae | Halieutaea fitzsimonsi | native | Circular seabat | |
| Lophiiformes | Ogcocephalidae | Halieutaea fumosa | native | Smoky seabat | Japanese : Hime-akagutsu |
| Lophiiformes | Ogcocephalidae | Halieutaea indica | native | Indian handfish | |
| Lophiiformes | Ogcocephalidae | Halieutaea stellata | native | Minipizza batfish | Japanese : Akagutsu |
| Lophiiformes | Ogcocephalidae | Halieutopsis bathyoreos | native | Broad-snout deepsea batfish | Japanese : Hira-mushi-furyu-uo |
| Lophiiformes | Ogcocephalidae | Halieutopsis margaretae | native | Margaret's deepsea batfish | |
| Lophiiformes | Ogcocephalidae | Halieutopsis nudiventer | native | Naked-belly deepsea batfish | |
| Lophiiformes | Ogcocephalidae | Halieutopsis oblonga | native | Oblong deepsea batfish | |
| Lophiiformes | Ogcocephalidae | Halieutopsis okamurai | native | Okamura's deepsea batfish | English : Okamura’s deepsea batfish |
| Lophiiformes | Ogcocephalidae | Halieutopsis stellifera | native | Starry deepsea batfish | |
| Tetraodontiformes | Triacanthodidae | Halimochirurgus alcocki | native | Japanese : Nagakawamuki | |
| Notacanthiformes | Halosauridae | Halosauropsis macrochir | native | Abyssal halosaur | Japanese : Kuroobi-tokagegisu |
| Acanthuriformes | Lobotidae | Hapalogenys analis | native | Broadbanded velvetchin | Japanese : Setodai; Japanese : Setodai; |
| Acanthuriformes | Lobotidae | Hapalogenys kishinouyei | native | Lined javelinfish | Japanese : Shima-setodai |
| Acanthuriformes | Lobotidae | Hapalogenys nigripinnis | native | Short barbeled velvetchin | Japanese : Higedai; Japanese : Higesoridai; |
| Acanthuriformes | Lobotidae | Hapalogenys sennin | native | Long barbeled grunter | Japanese : Higedai |
| Anguilliformes | Synaphobranchidae | Haptenchelys parviocularis | native | Small-eyed abyssal eel | Japanese : Ankoku-hora-anago |
| Aulopiformes | Synodontidae | Harpadon microchir | native | Japanese : Mizutengu | |
| Aulopiformes | Synodontidae | Harpadon nehereus | native | Bombay-duck | Japanese : Tenaga-mizutengu |
| Chimaeriformes | Rhinochimaeridae | Harriotta chaetirhamphus | native | ||
| Chimaeriformes | Rhinochimaeridae | Harriotta raleighana | native | Pacific longnose chimaera | Japanese : Yomino-tsukai |
| Gobiiformes | Gobiidae | Hazeus ammophilus | native | ||
| Gobiiformes | Gobiidae | Hazeus otakii | native | Scalyhead goby | Japanese : Yukatahaze |
| Blenniiformes | Tripterygiidae | Helcogramma aquila | native | Darktail triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma chica | native | Little hooded triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma ellioti | native | ||
| Blenniiformes | Tripterygiidae | Helcogramma fuscipectoris | native | Fourspot triplefin | Japanese : Kuro-masuku |
| Blenniiformes | Tripterygiidae | Helcogramma fuscopinna | native | Blackfin triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma hudsoni | native | Hudson's triplefin | Japanese : Naname-hebiginpo |
| Blenniiformes | Tripterygiidae | Helcogramma inclinata | native | Triangle triplefin | Japanese : Aya-hebiginpo |
| Blenniiformes | Tripterygiidae | Helcogramma nesion | native | ||
| Blenniiformes | Tripterygiidae | Helcogramma obtusirostris | native | Hotlips triplefin | Japanese : Kuro-masuku |
| Blenniiformes | Tripterygiidae | Helcogramma rhinoceros | native | Rhinocerus triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma striata | native | Tropical striped triplefin | |
| Blenniiformes | Tripterygiidae | Helcogramma trigloides | native | Scarf triplefin | Japanese : Aya-hebiginpo |
| Perciformes/Scorpaenoidei | Sebastidae | Helicolenus hilgendorfii | native | Japanese : Yumekasago | |
| Cypriniformes | Gobionidae | Hemibarbus labeo | native | Barbel steed | Japanese : Nigoi |
| Cypriniformes | Gobionidae | Hemibarbus longirostris | native | Japanese : Zunaga-nigoi | |
| Cypriniformes | Gobionidae | Hemibarbus maculatus | native | Spotted steed | |
| Cypriniformes | Xenocyprididae | Hemiculter leucisculus | native | Sharpbelly | |
| Carcharhiniformes | Hemigaleidae | Hemigaleus microstoma | native | Sicklefin weasel shark | |
| Ovalentaria/misc | Pomacentridae | Hemiglyphidodon plagiometopon | native | Lagoon damselfish | Japanese : Suzumedai-modoki |
| Cypriniformes | Xenocyprididae | Hemigrammocypris neglecta | native | Japanese : Kawabatamoroko | |
| Eupercaria/misc | Labridae | Hemigymnus fasciatus | native | Barred thicklip | Japanese : Shima-tarekuchi-bera |
| Eupercaria/misc | Labridae | Hemigymnus melapterus | native | Blackeye thicklip | Japanese : Tarekuchi-bera |
| Perciformes/Cottoidei | Cottidae | Hemilepidotus gilberti | native | Gilbert's Irish Lord | Japanese : Yokosujikajika |
| Perciformes/Cottoidei | Cottidae | Hemilepidotus jordani | native | Yellow Irish lord | Japanese : Name-yokosujikajika |
| Perciformes/Cottoidei | Cottidae | Hemilepidotus papilio | native | Butterfly sculpin | Japanese : Kujakukajika |
| Perciformes/Scorpaenoidei | Peristediidae | Heminodus philippinus | native | Japanese : Itokihôbô | |
| Beloniformes | Hemiramphidae | Hemiramphus far | native | Black-barred halfbeak | Japanese : Hoshi-zayori |
| Beloniformes | Hemiramphidae | Hemiramphus lutkei | native | Lutke's halfbeak | Japanese : Nanyô-sayori |
| Acanthuriformes | Chaetodontidae | Hemitaurichthys polylepis | native | Pyramid butterflyfish | Japanese : Kasumi-chôchô-uo |
| Acanthuriformes | Chaetodontidae | Hemitaurichthys thompsoni | native | Thompson's butterflyfish | |
| Carcharhiniformes | Triakidae | Hemitriakis complicofasciata | native | ||
| Carcharhiniformes | Triakidae | Hemitriakis japanica | native | Japanese topeshark | Japanese : Eirakubuka |
| Perciformes/Cottoidei | Agonidae | Hemitripterus villosus | native | Japanese : Kemushikajika | |
| Myliobatiformes | Dasyatidae | Hemitrygon akajei | native | Whip stingray | Japanese : Aka-ei |
| Myliobatiformes | Dasyatidae | Hemitrygon bennettii | native | Bennett's stingray | Japanese : Onaga-ei |
| Myliobatiformes | Dasyatidae | Hemitrygon izuensis | endemic | Izu stingray | Japanese : Izuhime-ei |
| Myliobatiformes | Dasyatidae | Hemitrygon laevigata | native | Yantai stingray | |
| Acanthuriformes | Chaetodontidae | Heniochus acuminatus | native | Pennant coralfish | Japanese : Hatatatedai |
| Acanthuriformes | Chaetodontidae | Heniochus chrysostomus | native | Pennant bannerfish | Japanese : Minami-hatatatedai |
| Acanthuriformes | Chaetodontidae | Heniochus diphreutes | native | False moorish idol | Japanese : Mure-hatatatedai |
| Acanthuriformes | Chaetodontidae | Heniochus monoceros | native | Masked bannerfish | Japanese : Oni-hatatatedai |
| Acanthuriformes | Chaetodontidae | Heniochus singularius | native | Singular bannerfish | Japanese : Shima-hatatatedai |
| Acanthuriformes | Chaetodontidae | Heniochus varius | native | Horned bannerfish | Japanese : Tsuno-hatatatedai |
| Hexanchiformes | Hexanchidae | Heptranchias perlo | native | Sharpnose sevengill shark | Japanese : Edo-aburazame |
| Clupeiformes | Dorosomatidae | Herklotsichthys quadrimaculatus | native | Bluestripe herring | Japanese : Mizun |
| Gobiiformes | Gobiidae | Hetereleotris exilis | native | Japanese : Sasagaki-haze | |
| Gobiiformes | Gobiidae | Hetereleotris poecila | native | Japanese : Shirozukinhaze | |
| Blenniiformes | Clinidae | Heteroclinus roseus | native | Rosy weedfish | Japanese : Beni-asahiginpo |
| Anguilliformes | Congridae | Heteroconger fugax | native | Shy garden eel | Japanese : Nigemizu-chin'anago |
| Anguilliformes | Congridae | Heteroconger hassi | native | Spotted garden-eel | Japanese : Chin-anago |
| Anguilliformes | Congridae | Heteroconger polyzona | native | Zebra garden eel | |
| Heterodontiformes | Heterodontidae | Heterodontus japonicus | native | Japanese bullhead shark | Japanese : Nekozame |
| Heterodontiformes | Heterodontidae | Heterodontus zebra | native | Zebra bullhead shark | Japanese : Shima-nekozame |
| Pleuronectiformes | Soleidae | Heteromycteris japonicus | native | Bamboo sole | |
| Pleuronectiformes | Soleidae | Heteromycteris matsubarai | native | Japanese : Montsuki-ushinoshita | |
| Stomiiformes | Stomiidae | Heterophotus ophistoma | native | Wingfin snaggletooth | Japanese : Ôtokagehadaka |
| Gobiiformes | Gobiidae | Heteroplopomus barbatus | native | Japanese : Niramihaze | |
| Eupercaria/misc | Priacanthidae | Heteropriacanthus carolinus | native | Indo-Pacific glasseye | |
| Cichliformes | Cichlidae | Heterotilapia buettikoferi | introduced | Zebra tilapia | |
| Perciformes/Cottoidei | Hexagrammidae | Hexagrammos agrammus | native | Spotty-bellied greenling | Japanese : Kujime |
| Perciformes/Cottoidei | Hexagrammidae | Hexagrammos lagocephalus | native | Rock greenling | Japanese : Usagi-ainame |
| Perciformes/Cottoidei | Hexagrammidae | Hexagrammos octogrammus | native | Masked greenling | Japanese : Suji-ainame |
| Perciformes/Cottoidei | Hexagrammidae | Hexagrammos otakii | native | Fat greenling | Japanese : Ainame |
| Perciformes/Cottoidei | Hexagrammidae | Hexagrammos stelleri | native | Whitespotted greenling | Japanese : Ezo-ainame |
| Hexanchiformes | Hexanchidae | Hexanchus griseus | native | Bluntnose sixgill shark | Japanese : Kagurazame |
| Hexanchiformes | Hexanchidae | Hexanchus nakamurai | native | Bigeyed sixgill shark | |
| Myliobatiformes | Hexatrygonidae | Hexatrygon bickelli | native | Sixgill stingray | Japanese : Mutsuera-ei |
| Lophiiformes | Himantolophidae | Himantolophus borealis | native | ||
| Lophiiformes | Himantolophidae | Himantolophus groenlandicus | native | Atlantic footballfish | Japanese : Chôchin-ankô |
| Lophiiformes | Himantolophidae | Himantolophus sagamius | native | Pacific footballfish | |
| Myliobatiformes | Dasyatidae | Himantura undulata | native | Leopard whipray | |
| Aulopiformes | Aulopidae | Hime japonica | native | Japanese thread-sail fish | Japanese : Hime |
| Syngnathiformes | Syngnathidae | Hippichthys cyanospilos | native | Blue-spotted pipefish | Japanese : Hakuten-yôji |
| Syngnathiformes | Syngnathidae | Hippichthys heptagonus | native | Belly pipefish | Japanese : Amime-kawa-yōji |
| Syngnathiformes | Syngnathidae | Hippichthys penicillus | native | Beady pipefish | Japanese : Ganten-ishi-yôji |
| Syngnathiformes | Syngnathidae | Hippichthys spicifer | native | Bellybarred pipefish | Japanese : Kawa-yôji |
| Syngnathiformes | Syngnathidae | Hippocampus bargibanti | native | Pygmy seahorse | |
| Syngnathiformes | Syngnathidae | Hippocampus coronatus | native | Crowned seahorse | Japanese : Tatsu-no-otoshigo |
| Syngnathiformes | Syngnathidae | Hippocampus haema | native | Korean seahorse | Japanese : Himetatsu |
| Syngnathiformes | Syngnathidae | Hippocampus histrix | native | Thorny seahorse | Japanese : Ibara-Tatsu |
| Syngnathiformes | Syngnathidae | Hippocampus japapigu | native | Japanese pygmy seahorse | Japanese : Hachijo-tatsu |
| Syngnathiformes | Syngnathidae | Hippocampus kelloggi | native | Great seahorse | Japanese : O-umi-uma |
| Syngnathiformes | Syngnathidae | Hippocampus kuda | native | Spotted seahorse | Japanese : Ô-umiuma |
| Syngnathiformes | Syngnathidae | Hippocampus mohnikei | native | Japanese seahorse | Japanese : Kitano-umi-uma |
| Syngnathiformes | Syngnathidae | Hippocampus pontohi | native | Pontoh's pygmy seahorse | |
| Syngnathiformes | Syngnathidae | Hippocampus sindonis | native | Shiho's seahorse | Japanese : Enshûtatsu |
| Syngnathiformes | Syngnathidae | Hippocampus trimaculatus | native | Longnose seahorse | Japanese : Takakuratatsu |
| Pleuronectiformes | Pleuronectidae | Hippoglossoides dubius | native | Flathead flounder | Japanese : Akagarei |
| Pleuronectiformes | Pleuronectidae | Hippoglossoides elassodon | native | Flathead sole | Japanese : Umagarei |
| Pleuronectiformes | Pleuronectidae | Hippoglossoides robustus | native | Bering flounder | Japanese : Dorogarei |
| Pleuronectiformes | Pleuronectidae | Hippoglossus stenolepis | native | Pacific halibut | Japanese : Ohyô |
| Eupercaria/misc | Scaridae | Hipposcarus longiceps | native | Pacific longnose parrotfish | Japanese : Kitsune-budai |
| Perciformes/Scorpaenoidei | Scorpaenidae | Hipposcorpaena filamentosa | native | Filamentous scorpionfish | Japanese : Itohiki-kasago |
| Beloniformes | Exocoetidae | Hirundichthys albimaculatus | native | Whitespot flyingfish | Japanese : Ôme-oki-tobi |
| Beloniformes | Exocoetidae | Hirundichthys oxycephalus | native | Bony flyingfish | Japanese : Hoso-ao-tobi |
| Beloniformes | Exocoetidae | Hirundichthys rondeletii | native | Black wing flyingfish | Japanese : Oki-tobi |
| Beloniformes | Exocoetidae | Hirundichthys speculiger | native | Mirrorwing flyingfish | Japanese : Ninoji-tobi-uo |
| Anguilliformes | Synaphobranchidae | Histiobranchus bathybius | native | Deep-water arrowtooth eel | Japanese : Soko-anago |
| Acropomatiformes | Pentacerotidae | Histiopterus typus | native | Sailfin armourhead | Japanese : Kawabisha |
| Lophiiformes | Antennariidae | Histrio histrio | native | Sargassumfish | Japanese : Hanaokoze |
| Eupercaria/misc | Labridae | Hologymnosus annulatus | native | Ring wrasse | Japanese : Namerabera |
| Eupercaria/misc | Labridae | Hologymnosus doliatus | native | Pastel ringwrasse | Japanese : Shirotasukibera |
| Eupercaria/misc | Labridae | Hologymnosus rhodonotus | native | Redback longface wrasse | |
| Alepocephaliformes | Platytroctidae | Holtbyrnia innesi | native | Teardrop tubeshoulder | |
| Ophidiiformes | Ophidiidae | Homostolus acer | native | Filament cusk | Japanese : Itohiki-itachiuo |
| Perciformes/Scorpaenoidei | Hoplichthyidae | Hoplichthys fasciatus | native | Japanese : Shima-harigochi | |
| Perciformes/Scorpaenoidei | Hoplichthyidae | Hoplichthys filamentosus | native | Longray ghost flathead | Japanese : Ito-harigochi |
| Perciformes/Scorpaenoidei | Hoplichthyidae | Hoplichthys gilberti | native | Japanese : Soko-harigochi | |
| Perciformes/Scorpaenoidei | Hoplichthyidae | Hoplichthys langsdorfii | native | Japanese : Natsu-harigochi | |
| Perciformes/Scorpaenoidei | Hoplichthyidae | Hoplichthys regani | native | Ghost flathead | Japanese : Harigochi |
| Ophidiiformes | Ophidiidae | Hoplobrotula armata | native | Armoured cusk | Japanese : Yoroi-itachiuo |
| Ophidiiformes | Ophidiidae | Hoplobrotula badia | native | Japanese : Kuro-yoroi-itachiuo | |
| Eupercaria/misc | Malacanthidae | Hoplolatilus cuniculus | native | Dusky tilefish | Japanese : Okinawa-sango-amadai |
| Perciformes/Scorpaenoidei | Scorpaenidae | Hoplosebastes armatus | native | Japanese : Hana-kasago | |
| Trachichthyiformes | Trachichthyidae | Hoplostethus crassispinus | native | Japanese : Maru-hiuchidai | |
| Trachichthyiformes | Trachichthyidae | Hoplostethus japonicus | native | Western Pacific roughy | Japanese : Hiuchidai |
| Trachichthyiformes | Trachichthyidae | Hoplostethus melanopus | native | Smallscale slimehead | |
| Trachichthyiformes | Trachichthyidae | Hoplostethus robustispinus | native | Thickspine roughy | |
| Acropomatiformes | Howellidae | Howella parini | native | Japanese : Kushi-sumikui-uo | |
| Acropomatiformes | Howellidae | Howella zina | native | Japanese : Togekushi-sumikui-uo | |
| Perciformes/Scorpaenoidei | Sebastidae | Hozukius emblemarius | native | Japanese : Hôzuki | |
| Acipenseriformes | Acipenseridae | Huso dauricus | native | Kaluga | Japanese : Dauria-chôzame |
| Chimaeriformes | Chimaeridae | Hydrolagus barbouri | native | Japanese : Kokonohoshi-ginzame | |
| Chimaeriformes | Chimaeridae | Hydrolagus eidolon | native | Japanese : Niji-ginzame | |
| Chimaeriformes | Chimaeridae | Hydrolagus mitsukurii | native | Spookfish | Japanese : Aka-ginzame |
| Chimaeriformes | Chimaeridae | Hydrolagus purpurescens | native | Purple chimaera | Japanese : Murasaki-ginzame |
| Myctophiformes | Myctophidae | Hygophum proximum | native | Firefly lanternfish | Japanese : Tsumari-donguri-hadaka |
| Myctophiformes | Myctophidae | Hygophum reinhardtii | native | Reinhardt's lantern fish | Japanese : Donguri-hadaka |
| Gadiformes | Macrouridae | Hymenocephalus hachijoensis | native | Japanese : Hachijô-sokodara | |
| Gadiformes | Macrouridae | Hymenocephalus lethonemus | native | Japanese : Itodara | |
| Gadiformes | Macrouridae | Hymenocephalus longiceps | native | Japanese : Wanidara | |
| Gadiformes | Macrouridae | Hymenocephalus papyraceus | native | Japanese : Kamidara | |
| Gadiformes | Macrouridae | Hymenocephalus striatissimus | native | Japanese : Sujidara | |
| Gadiformes | Macrouridae | Hymenocephalus yamasakiorum | native | Black-tailed membranehead | Japanese : Oguro-sujidara |
| Gadiformes | Macrouridae | Hymenogadus gracilis | native | Slender membranehead | Japanese : Oni-sujidara |
| Scombriformes | Centrolophidae | Hyperoglyphe japonica | native | Pacific barrelfish | Japanese : Medai |
| Atheriniformes | Atherinidae | Hypoatherina barnesi | native | Barnes' silverside | |
| Atheriniformes | Atherinidae | Hypoatherina lunata | native | Okinawan silverside | Japanese : Okinawa-togoro |
| Atheriniformes | Atherinidae | Hypoatherina tsurugae | native | Japanese : Gin-iso-iwashi | |
| Atheriniformes | Atherinidae | Hypoatherina valenciennei | native | Sumatran silverside | Japanese : Tôgôrô-iwashi |
| Atheriniformes | Atherinidae | Hypoatherina woodwardi | native | Japanese : Okinawa-tôgorô | |
| Carcharhiniformes | Triakidae | Hypogaleus hyugaensis | native | Blacktip tope | Japanese : Tsumaguro-eirakubuka |
| Osmeriformes | Osmeridae | Hypomesus japonicus | native | Japanese : Chika | |
| Osmeriformes | Osmeridae | Hypomesus nipponensis | native | Japanese smelt | Japanese : Chishima wakasagi; Japanese : Wakasagi; |
| Osmeriformes | Osmeridae | Hypomesus olidus | native | Pond smelt | Japanese : Ishikarai-wakasagi |
| Cypriniformes | Xenocyprididae | Hypophthalmichthys molitrix | introduced | Silver carp | Japanese : Hakuren |
| Cypriniformes | Xenocyprididae | Hypophthalmichthys nobilis | introduced | Bighead carp | Japanese : Kokuren |
| Perciformes/Gasterosteoidei | Hypoptychidae | Hypoptychus dybowskii | native | Korean sandlance | Japanese : Shiwa-ikanago |
| Beloniformes | Hemiramphidae | Hyporhamphus affinis | native | Tropical halfbeak | |
| Beloniformes | Hemiramphidae | Hyporhamphus intermedius | native | Asian pencil halfbeak | Japanese : Kurume-sayori |
| Beloniformes | Hemiramphidae | Hyporhamphus quoyi | native | Quoy's garfish | Japanese : Sennin-sayori |
| Beloniformes | Hemiramphidae | Hyporhamphus sajori | native | Japanese halfbeak | Japanese : Sayori |
| Perciformes/Serranoidei | Epinephelidae | Hyporthodus octofasciatus | native | Eightbar grouper | Japanese : Mahata-modoki |
| Perciformes/Serranoidei | Epinephelidae | Hyporthodus septemfasciatus | native | Convict grouper | Japanese : Mahata |
| Perciformes/Cottoidei | Agonidae | Hypsagonus quadricornis | native | Fourhorn poacher | Japanese : Tsuno-shachi-uo |
| Gobiiformes | Eleotridae | Hypseleotris cyprinoides | native | Tropical carp-gudgeon | Japanese : Tanago-modoki |
| Perciformes/Cottoidei | Cottidae | Icelinus japonicus | native | Japanese : Futasujikajika | |
| Perciformes/Cottoidei | Cottidae | Icelus canaliculatus | native | Blacknose sculpin | Japanese : Kuro-kôrikajika |
| Perciformes/Cottoidei | Cottidae | Icelus cataphractus | native | Japanese : Kôrikajika | |
| Perciformes/Cottoidei | Cottidae | Icelus ecornis | native | Japanese : Chigo-kōrikajika | |
| Perciformes/Cottoidei | Cottidae | Icelus gilberti | native | Japanese : Daruma-kôrikajika | |
| Perciformes/Cottoidei | Cottidae | Icelus mandibularis | native | Japanese : Ukekuchi-kôrikajika | |
| Perciformes/Cottoidei | Cottidae | Icelus perminovi | native | Scaly-belly sculpin | Japanese : Fusa-kôrikajika |
| Perciformes/Cottoidei | Cottidae | Icelus sekii | native | Japanese : Rausu-kajika | |
| Perciformes/Cottoidei | Cottidae | Icelus stenosomus | native | ||
| Perciformes/Cottoidei | Cottidae | Icelus toyamensis | native | Japanese : Tomi-kajika | |
| Anguilliformes | Ophichthidae | Ichthyapus keramanus | native | ||
| Anguilliformes | Ophichthidae | Ichthyapus vulturis | native | Vulture sand eel | Japanese : Togari-umihebi |
| Stomiiformes | Phosichthyidae | Ichthyococcus elongatus | native | Slim lightfish | Japanese : Shinju-eso |
| Perciformes/Uranoscopoidei | Uranoscopidae | Ichthyscopus pollicaris | native | Oriental fringe stargazer | Japanese : サツオミシマ |
| Scombriformes | Centrolophidae | Icichthys lockingtoni | native | Medusafish | |
| Scombriformes | Icosteidae | Icosteus aenigmaticus | native | Ragfish | |
| Siluriformes | Ictaluridae | Ictalurus punctatus | introduced | Channel catfish | |
| Stomiiformes | Stomiidae | Idiacanthus antrostomus | native | Pacific blackdragon | Japanese : Mitsumatayariuo |
| Stomiiformes | Stomiidae | Idiacanthus fasciola | native | Ribbon sawtail fish | Japanese : Nanyô-mitsumatayariuo |
| Myctophiformes | Myctophidae | Idiolychnus urolampus | native | Japanese : Ojiro-hadaka | |
| Ateleopodiformes | Ateleopodidae | Ijimaia dofleini | native | Japanese : Ô-shachiburi | |
| Ateleopodiformes | Ateleopodidae | Ijimaia fowleri | endemic | ||
| Clupeiformes | Pristigasteridae | Ilisha elongata | native | Elongate ilisha | Japanese : Hira |
| Anguilliformes | Synaphobranchidae | Ilyophis brunneus | native | Muddy arrowtooth eel | Japanese : Ryukyu-hora-anago |
| Anguilliformes | Synaphobranchidae | Ilyophis nigeli | native | ||
| Perciformes/Scorpaenoidei | Platycephalidae | Inegocia japonica | native | Japanese flathead | Japanese : Tokagegochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Inegocia ochiaii | native | English : Spot eye flathead | |
| Eupercaria/misc | Labridae | Iniistius aneitensis | native | Yellowblotch razorfish | Japanese : Hage-hirabera |
| Eupercaria/misc | Labridae | Iniistius baldwini | native | Baldwin's razorfish | |
| Eupercaria/misc | Labridae | Iniistius dea | native | Blackspot razorfish | Japanese : Tensu |
| Eupercaria/misc | Labridae | Iniistius evides | native | Japanese : Hoshi-hirabera | |
| Eupercaria/misc | Labridae | Iniistius geisha | native | Geisha razorfish | |
| Eupercaria/misc | Labridae | Iniistius melanopus | native | Yellowpatch razorfish | Japanese : Mon-hirabera |
| Eupercaria/misc | Labridae | Iniistius pavo | native | Peacock wrasse | Japanese : Hoshi-tensu; Japanese : Kuro-tensu; |
| Eupercaria/misc | Labridae | Iniistius pentadactylus | native | Fivefinger wrasse | Japanese : Hirabera |
| Eupercaria/misc | Labridae | Iniistius twistii | native | Redblotch razorfish | Japanese : Hinomaru-tensu |
| Eupercaria/misc | Labridae | Iniistius verrens | native | Japanese : Bara-hirabera | |
| Perciformes/Scorpaenoidei | Synanceiidae | Inimicus didactylus | native | Bearded ghoul | Japanese : Hime-oniokoze |
| Perciformes/Scorpaenoidei | Synanceiidae | Inimicus japonicus | native | Japanese : Oniokoze | |
| Perciformes/Scorpaenoidei | Synanceiidae | Inimicus joubini | native | Japanese : Seto-oniokoze | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Iracundus signifer | native | Decoy scorpionfish | Japanese : Hatatatekasago |
| Cypriniformes | Xenocyprididae | Ischikauia steenackeri | native | Japanese : Wataka | |
| Squaliformes | Dalatiidae | Isistius brasiliensis | native | Cookie cutter shark | Japanese : Darumazame |
| Squaliformes | Dalatiidae | Isistius plutodus | native | Largetooth cookiecutter shark | Japanese : Kohire-darumazame |
| Atheriniformes | Isonidae | Iso flosmaris | native | Japanese : Naminohana | |
| Atheriniformes | Isonidae | Iso rhothophilus | native | Flower of the wave | |
| Blenniiformes | Blenniidae | Istiblennius dussumieri | native | Streaky rockskipper | |
| Blenniiformes | Blenniidae | Istiblennius edentulus | native | Rippled rockskipper | Japanese : Nise-kaeru-uo |
| Blenniiformes | Blenniidae | Istiblennius lineatus | native | Lined rockskipper | Japanese : Sen-kaeru-uo |
| Gobiiformes | Gobiidae | Istigobius campbelli | native | Japanese : Kutsuwahaze | |
| Gobiiformes | Gobiidae | Istigobius decoratus | native | Decorated goby | Japanese : Hoshi-kazarihaze |
| Gobiiformes | Gobiidae | Istigobius goldmanni | native | Goldman's goby | Japanese : Hime-kazarihaze |
| Gobiiformes | Gobiidae | Istigobius hoshinonis | native | Japanese : Hoshinohaze | |
| Gobiiformes | Gobiidae | Istigobius ornatus | native | Ornate goby | Japanese : Kazarihaze |
| Gobiiformes | Gobiidae | Istigobius rigilius | native | Rigilius goby | Japanese : Madara-kazarihaze |
| Carangiformes | Istiophoridae | Istiompax indica | native | Black marlin | Japanese : Kurokawa |
| Carangiformes | Istiophoridae | Istiophorus platypterus | native | Indo-Pacific sailfish | Japanese : Bashôkajiki |
| Lamniformes | Lamnidae | Isurus oxyrinchus | native | Shortfin mako | Japanese : Aozame |
| Lamniformes | Lamnidae | Isurus paucus | native | Longfin mako | Japanese : Bake-aozame |
| Anguilliformes | Congridae | Japonoconger sivicolus | native | Japanese : Minami-anago | |
| Pleuronectiformes | Bothidae | Japonolaeops dentatus | native | Japanese : Hinadarumagarei | |
| Perciformes/Zoarcoidei | Zoarcidae | Japonolycodes abei | native | Japanese : Abegenge | |
| Kurtiformes | Apogonidae | Jaydia carinatus | native | Ocellate cardinalfish | Japanese : Mato-ishimochi |
| Kurtiformes | Apogonidae | Jaydia ellioti | native | Flag-in cardinal-fish | Japanese : Tsumaguro-ishimochi |
| Kurtiformes | Apogonidae | Jaydia lineata | native | Indian perch | Japanese : Tenjikudai |
| Kurtiformes | Apogonidae | Jaydia poeciloptera | native | Pearly-finned cardinalfish | |
| Kurtiformes | Apogonidae | Jaydia truncata | native | Flagfin cardinalfish | Japanese : Ufuni |
| Eupercaria/misc | Sciaenidae | Johnius amblycephalus | native | Bearded croaker | |
| Eupercaria/misc | Sciaenidae | Johnius belangerii | native | Belanger's croaker | Japanese : Konibe |
| Eupercaria/misc | Sciaenidae | Johnius distinctus | native | Japanese : Abura-guchi | |
| Eupercaria/misc | Sciaenidae | Johnius grypotus | native | Japanese : Konibe | |
| Carangiformes | Carangidae | Kaiwarinus equula | native | Whitefin trevally | Japanese : Kaiwari |
| Carangiformes | Istiophoridae | Kajikia audax | native | Striped marlin | Japanese : Makajiki |
| Scombriformes | Chiasmodontidae | Kali indica | native | ||
| Pleuronectiformes | Bothidae | Kamoharaia megastoma | native | Wide-mouthed flounder | Japanese : Wanigarei |
| Perciformes/Scorpaenoidei | Aploactinidae | Kanekonia florida | endemic | Japanese : Hanachigo-okoze | |
| Scombriformes | Scombridae | Katsuwonus pelamis | native | Skipjack tuna | Japanese : Katsuo |
| Anguilliformes | Chlopsidae | Kaupichthys atronasus | native | Black-nostril false moray | Japanese : Kurohige-iwa-anago |
| Anguilliformes | Chlopsidae | Kaupichthys hyoproroides | native | False moray | Japanese : Iwa-anago |
| Anguilliformes | Chlopsidae | Kaupichthys japonicus | native | ||
| Gobiiformes | Gobiidae | Kelloggella cardinalis | native | Cardinal goby | Japanese : Akahire-hadakahaze |
| Gobiiformes | Gobiidae | Kelloggella quindecimfasciata | native | Central goby | Japanese : Hadakahaze |
| Tetraodontiformes | Aracanidae | Kentrocapros aculeatus | native | Japanese : Itomakifugu | |
| Tetraodontiformes | Aracanidae | Kentrocapros flavofasciatus | native | Japanese : Kisuji-itomakifugu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Kochichthys flavofasciatus | native | Japanese : Kisujitoragisu | |
| Clupeiformes | Dorosomatidae | Konosirus punctatus | native | Dotted gizzard shad | Japanese : Konoshiro |
| Gobiesociformes | Gobiesocidae | Kopua japonica | native | Japanese deepwater clingfish | English : Japanese deepwater clingfish |
| Gobiesociformes | Gobiesocidae | Kopua vermiculata | native | Twilight clingfish | Japanese : Misaki-yozakura-ubauo |
| Gobiiformes | Gobiidae | Koumansetta hectori | native | Hector's goby | Japanese : Kinsenhaze |
| Gobiiformes | Kraemeriidae | Kraemeria cunicularia | native | Transparent sand dart | Japanese : Sunahaze |
| Gobiiformes | Kraemeriidae | Kraemeria tongaensis | native | Japanese : Tonga-sunahaze | |
| Perciformes/Zoarcoidei | Zoarcidae | Krusensterniella maculata | native | Maculated prickled eelpout | Japanese : Ai-haregaji |
| Perciformes/Zoarcoidei | Zoarcidae | Krusensterniella multispinosa | native | Multispine prickled eelpout | Japanese : Togegenge |
| Perciformes/Zoarcoidei | Zoarcidae | Krusensterniella notabilis | native | Notable prickled eelpout | Japanese : Haregaji |
| Perciformes/Zoarcoidei | Zoarcidae | Krusensterniella pseudomaculata | native | Tricksy prickled eelpout | |
| Perciformes/Zoarcoidei | Zoarcidae | Krusensterniella squamosa | native | Scaly prickled eelpout | English : Scaly prickled eelpout |
| Centrarchiformes | Kuhliidae | Kuhlia marginata | native | Dark-margined flagtail | Japanese : Yugoi |
| Centrarchiformes | Kuhliidae | Kuhlia mugil | native | Barred flagtail | Japanese : Gin-yugoi |
| Centrarchiformes | Kuhliidae | Kuhlia munda | native | Silver flagtail | Japanese : Togenaga-yugoi |
| Centrarchiformes | Kuhliidae | Kuhlia rupestris | native | Rock flagtail | Japanese : Okuchi-yugoi |
| Centrarchiformes | Kuhliidae | Kuhlia sandvicensis | native | Hawaiian flagtail | |
| Gadiformes | Macrouridae | Kumba japonica | native | Japanese : Kagami-hige | |
| Perciformes/Scorpaenoidei | Platycephalidae | Kumococius rodericensis | native | Spiny flathead | Japanese : Kumogochi |
| Gadiformes | Macrouridae | Kuronezumia darus | native | Japanese : Suruga-nezumidara | |
| Gadiformes | Macrouridae | Kuronezumia endoi | native | Japanese : Kuro-nezumi-dara | |
| Centrarchiformes | Kyphosidae | Kyphosus bigibbus | native | Brown chub | Japanese : Minami-isuzumi |
| Centrarchiformes | Kyphosidae | Kyphosus cinerascens | native | Blue sea chub | Japanese : Tenjikuisaki |
| Centrarchiformes | Kyphosidae | Kyphosus ocyurus | native | Bluestriped chub | Japanese : Koshinaga-isuzumi |
| Centrarchiformes | Kyphosidae | Kyphosus pacificus | native | Pacific drummer | |
| Centrarchiformes | Kyphosidae | Kyphosus vaigiensis | native | Brassy chub | Japanese : Isuzumi |
| Ovalentaria/misc | Pseudochromidae | Labracinus cyclophthalmus | native | Fire-tail devil | Japanese : Megisu |
| Centrarchiformes | Scorpididae | Labracoglossa argenteiventris | native | Japanese : Takabe | |
| Eupercaria/misc | Labridae | Labrichthys unilineatus | native | Tubelip wrasse | Japanese : Kurobera |
| Eupercaria/misc | Labridae | Labroides bicolor | native | Bicolor cleaner wrasse | Japanese : Somewakebera |
| Eupercaria/misc | Labridae | Labroides dimidiatus | native | Bluestreak cleaner wrasse | Japanese : Hon-somewakebera |
| Eupercaria/misc | Labridae | Labroides pectoralis | native | Blackspot cleaner wrasse | Japanese : Sumitsuki-somewakebera |
| Eupercaria/misc | Labridae | Labropsis manabei | native | Northern tubelip | Japanese : Manabebera |
| Eupercaria/misc | Labridae | Labropsis xanthonota | native | Yellowback tubelip | Japanese : Miyakebera |
| Carangaria/misc | Lactariidae | Lactarius lactarius | native | False trevally | Japanese : Akuta-uo |
| Tetraodontiformes | Ostraciidae | Lactoria cornuta | native | Longhorn cowfish | Japanese : Kongô-fugu |
| Tetraodontiformes | Ostraciidae | Lactoria diaphana | native | Roundbelly cowfish | Japanese : Umisuzume |
| Tetraodontiformes | Ostraciidae | Lactoria fornasini | native | Thornback cowfish | Japanese : Shima-umisuzume |
| Gadiformes | Moridae | Laemonema filodorsale | native | Japanese : Hotei-itohikidara | |
| Gadiformes | Moridae | Laemonema longipes | native | Longfin codling | Japanese : Itohikidara |
| Gadiformes | Moridae | Laemonema modestum | native | Japanese : Kurodara | |
| Gadiformes | Moridae | Laemonema nana | native | Japanese : Himedara | |
| Gadiformes | Moridae | Laemonema rhodochir | native | Japanese : Palao-itohikidara | |
| Pleuronectiformes | Bothidae | Laeops kitaharae | native | Japanese : Yarigarei | |
| Pleuronectiformes | Bothidae | Laeops lanceolata | native | ||
| Pleuronectiformes | Bothidae | Laeops nigromaculatus | native | Blackspotted flounder | Japanese : Hoshi-yarigarei |
| Pleuronectiformes | Bothidae | Laeops parviceps | native | Small headed flounder | |
| Tetraodontiformes | Tetraodontidae | Lagocephalus gloveri | native | Japanese : Kuro-sabafugu | |
| Tetraodontiformes | Tetraodontidae | Lagocephalus guentheri | native | Diamondback puffer | |
| Tetraodontiformes | Tetraodontidae | Lagocephalus inermis | native | Smooth blaasop | Japanese : Kanafugu |
| Tetraodontiformes | Tetraodontidae | Lagocephalus lagocephalus | native | Oceanic puffer | Japanese : Kumasakafugu |
| Tetraodontiformes | Tetraodontidae | Lagocephalus lunaris | native | Lunartail puffer | Japanese : Doku-sabafugu |
| Tetraodontiformes | Tetraodontidae | Lagocephalus sceleratus | native | Silver-cheeked toadfish | Japanese : Sen-ninfugu |
| Tetraodontiformes | Tetraodontidae | Lagocephalus wheeleri | native | Japanese : Shiro-sabafugu | |
| Blenniiformes | Blenniidae | Laiphognathus longispinis | native | Crown spotty blenny | Japanese : Madara-gimpo |
| Blenniiformes | Blenniidae | Laiphognathus multimaculatus | native | Spotty blenny | |
| Lamniformes | Lamnidae | Lamna ditropis | native | Salmon shark | Japanese : Nezumizame |
| Anguilliformes | Ophichthidae | Lamnostoma polyophthalmum | native | Ocellated sand-eel | |
| Myctophiformes | Myctophidae | Lampadena luminosa | native | Luminous lanternfish | Japanese : Kagami-iwashi |
| Myctophiformes | Myctophidae | Lampadena urophaos | native | Sunbeam lampfish | Japanese : Hotarubi-hadaka |
| Myctophiformes | Myctophidae | Lampadena yaquinae | native | Japanese : Sankô-hadaka | |
| Myctophiformes | Myctophidae | Lampanyctus acanthurus | native | Spinytail lampfish | Japanese : Ôme-niji-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus alatus | native | Winged lanternfish | Japanese : Tomi-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus fernae | native | ||
| Myctophiformes | Myctophidae | Lampanyctus festivus | native | Festive lanternfish | Japanese : Niji-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus hawaiiensis | native | Japanese : Tenashi-hadaka | |
| Myctophiformes | Myctophidae | Lampanyctus jordani | native | Brokenline lanternfish | Japanese : Mame-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus niger | native | Black lantern fish | Japanese : Tongari-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus nobilis | native | Noble lampfish | Japanese : Hoso-tongari-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus regalis | native | Pinpoint lampfish | Japanese : Mikado-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus simulator | native | Japanese : Hoso-mame-hadaka | |
| Myctophiformes | Myctophidae | Lampanyctus tenuiformis | native | Slender lanternfish | Japanese : Nettai-niji-hadaka |
| Myctophiformes | Myctophidae | Lampanyctus turneri | native | Japanese : Kata-hadaka | |
| Ophidiiformes | Ophidiidae | Lamprogrammus brunswigi | native | ||
| Eupercaria/misc | Sciaenidae | Larimichthys crocea | native | Large yellow croaker | Japanese : Fûsei |
| Eupercaria/misc | Sciaenidae | Larimichthys polyactis | native | Yellow croaker | Japanese : Ki-guchi |
| Acropomatiformes | Lateolabracidae | Lateolabrax japonicus | native | Japanese seabass | Japanese : Suzuki |
| Acropomatiformes | Lateolabracidae | Lateolabrax latus | native | Blackfin seabass | Japanese : Hira-suzuki |
| Carangaria/misc | Latidae | Lates calcarifer | native | Barramundi | Japanese : Akame |
| Carangaria/misc | Latidae | Lates japonicus | endemic | Japanese lates | Japanese : Okinokoi |
| Cypriniformes | Nemacheilidae | Lefua echigonia | native | Japanese : Hotokedojô | |
| Cypriniformes | Nemacheilidae | Lefua nikkonis | endemic | Japanese : Ezo-hotokedojô | |
| Cypriniformes | Nemacheilidae | Lefua nishimurai | native | Japanese : Reihoku-nagare-hotoke-dojyô | |
| Cypriniformes | Nemacheilidae | Lefua torrentis | native | ||
| Acanthuriformes | Leiognathidae | Leiognathus equula | native | Common ponyfish | Japanese : Seitaka-hiiragi |
| Acanthuriformes | Leiognathidae | Leiognathus parviceps | native | ||
| Anguilliformes | Ophichthidae | Leiuranus semicinctus | native | Saddled snake-eel | Japanese : Sora-umihebi |
| Gobiiformes | Gobiidae | Lentipes armatus | native | Peppermint armour goby | Japanese : Yoroi-bôzuhaze |
| Gobiiformes | Gobiidae | Lentipes bunagaya | native | Bunagaya goby | Japanese : Bunagaya-bouzu-haze |
| Gobiiformes | Gobiidae | Lentipes kijimuna | native | Kijimuna goby | Japanese : Kijimunâ-bouzu-haze |
| Gobiesociformes | Gobiesocidae | Lepadichthys trishula | native | Trident clingfsh | Japanese : Minami-ubauo |
| Gadiformes | Moridae | Lepidion inosimae | native | Morid cod | Japanese : Soko-kurodara |
| Gadiformes | Moridae | Lepidion schmidti | native | Schmidt's cod | Japanese : Kita-no-kurodara |
| Pleuronectiformes | Citharidae | Lepidoblepharon ophthalmolepis | native | Scale-eyed flounder | Japanese : Uroko-garei |
| Scombriformes | Gempylidae | Lepidocybium flavobrunneum | native | Escolar | Japanese : Aburasokomutsu |
| Pleuronectiformes | Pleuronectidae | Lepidopsetta bilineata | native | Pacific rock sole | Japanese : Shumushugarei |
| Pleuronectiformes | Pleuronectidae | Lepidopsetta mochigarei | native | Dusky sole | Japanese : Asabagarei |
| Pleuronectiformes | Pleuronectidae | Lepidopsetta polyxystra | native | Northern rock sole | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla abyssalis | native | Japanese : Soko-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla alata | native | Japanese : Igodakahoderi | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla guentheri | native | Japanese : Kanado | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla hime | native | Japanese : Hime-soko-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla japonica | native | Japanese : Toge-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla kanagashira | native | Japanese : Hirenaga-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla kishinouyi | native | Japanese : Oni-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla longifaciata | native | Japanese : Tsuranaga-soko-kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla microptera | native | Japanese : Kanagashira | |
| Perciformes/Scorpaenoidei | Triglidae | Lepidotrigla punctipectoralis | native | Finspot gurnard | Japanese : Hirehoshi-kanagashira |
| Ovalentaria/misc | Pomacentridae | Lepidozygus tapeinosoma | native | Fusilier damselfish | Japanese : Hanadai-damashi |
| Centrarchiformes | Centrarchidae | Lepomis macrochirus | introduced | Bluegill | Japanese : Burûgiru |
| Lophiiformes | Oneirodidae | Leptacanthichthys gracilispinis | native | Plainchin dreamarm | |
| Aulopiformes | Aulopidae | Leptaulopus damasi | native | Japanese : Esodamasi | |
| Alepocephaliformes | Alepocephalidae | Leptochilichthys microlepis | native | Smallscale smoothhead | Japanese : Oni-iwashi |
| Alepocephaliformes | Alepocephalidae | Leptoderma lubricum | native | Japanese : Namera-iwashi | |
| Alepocephaliformes | Alepocephalidae | Leptoderma retropinna | native | Japanese : Yase-namera-iwashi | |
| Eupercaria/misc | Scaridae | Leptoscarus vaigiensis | native | Marbled parrotfish | Japanese : Mizorebudai |
| Perciformes/Zoarcoidei | Eulophiidae | Leptostichaeus pumilus | native | Neck banded blenny | |
| Stomiiformes | Stomiidae | Leptostomias multifilis | native | Japanese : Yari-hoshi-eso | |
| Stomiiformes | Stomiidae | Leptostomias robustus | native | Japanese : Fude-hoshi-eso | |
| Scombriformes | Trichiuridae | Lepturacanthus savala | native | Savalai hairtail | |
| Aulopiformes | Paralepididae | Lestidiops indopacificus | native | Indo-Pacific barracudina | Japanese : Nettai-name-hadaka |
| Aulopiformes | Paralepididae | Lestidiops jayakari | native | Pacific barracudina | Japanese : Shiro-name-hadaka |
| Aulopiformes | Paralepididae | Lestidiops sphyraenopsis | native | Japanese : Yase-hadaka-eso | |
| Aulopiformes | Paralepididae | Lestidium atlanticum | native | Atlantic barracudina | Japanese : Hitosuji-name-hadaka |
| Aulopiformes | Paralepididae | Lestidium prolixum | native | Japanese : Name-hadaka | |
| Aulopiformes | Paralepididae | Lestrolepis intermedia | native | Japanese : Futasuji-name-hadaka | |
| Aulopiformes | Paralepididae | Lestrolepis japonica | native | Japanese barracudina | Japanese : Hadaka-eso |
| Aulopiformes | Paralepididae | Lestrolepis nigroventralis | native | Black-belly barracudina | English : Black-belly barracudina |
| Aulopiformes | Paralepididae | Lestrolepis pofi | native | ||
| Petromyzontiformes | Petromyzontidae | Lethenteron camtschaticum | native | Arctic lamprey | Japanese : Kawa-yatsume |
| Petromyzontiformes | Petromyzontidae | Lethenteron hattai | native | Southern Japanese brook lamprey | |
| Petromyzontiformes | Petromyzontidae | Lethenteron kessleri | native | Siberian brook lamprey | Japanese : Shiberia yatsume |
| Petromyzontiformes | Petromyzontidae | Lethenteron mitsukurii | native | ||
| Petromyzontiformes | Petromyzontidae | Lethenteron reissneri | native | Far Eastern brook lamprey | Japanese : Suna-yatsume |
| Petromyzontiformes | Petromyzontidae | Lethenteron satoi | endemic | Fan-tailed brook lamprey | |
| Eupercaria/misc | Lethrinidae | Lethrinus amboinensis | native | Ambon emperor | Japanese : Yokoshima-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus atkinsoni | native | Pacific yellowtail emperor | Japanese : Iso-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus erythracanthus | native | Orange-spotted emperor | Japanese : Ama-kuchibi |
| Eupercaria/misc | Lethrinidae | Lethrinus genivittatus | native | Longspine emperor | Japanese : Ito-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus haematopterus | native | Chinese emperor | Japanese : Fuefuki-dai |
| Eupercaria/misc | Lethrinidae | Lethrinus harak | native | Thumbprint emperor | Japanese : Mato-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus lentjan | native | Pink ear emperor | Japanese : Shimofuri-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus microdon | native | Smalltooth emperor | Japanese : Ô-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus miniatus | native | Trumpet emperor | Japanese : Amami-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus nebulosus | native | Spangled emperor | Japanese : Hama-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus obsoletus | native | Orange-striped emperor | Japanese : Tateshima-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus olivaceus | native | Longface emperor | Japanese : Kitsune-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus ornatus | native | Ornate emperor | Japanese : Hana-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus ravus | native | Drab emperor | |
| Eupercaria/misc | Lethrinidae | Lethrinus reticulatus | native | Red snout emperor | Japanese : Yaeyama-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus rubrioperculatus | native | Spotcheek emperor | Japanese : Hôaka-kuchibi; Japanese : Muru; |
| Eupercaria/misc | Lethrinidae | Lethrinus semicinctus | native | Blackblotch emperor | Japanese : Ami-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus variegatus | native | Slender emperor | Japanese : Hoso-fuefuki |
| Eupercaria/misc | Lethrinidae | Lethrinus xanthochilus | native | Yellowlip emperor | Japanese : Muneaka-kuchibi |
| Gobiiformes | Gobiidae | Leucopsarion petersii | native | Ice goby | Japanese : Shiro-uo |
| Argentiniformes | Bathylagidae | Leuroglossus schmidti | native | Northern smoothtongue | Japanese : Togari-ichimonji-iwashi |
| Pleuronectiformes | Soleidae | Liachirus melanospilos | native | Carpet sole | Japanese : Garasu-ushinoshita |
| Pleuronectiformes | Pleuronectidae | Limanda aspera | native | Yellowfin sole | Japanese : Koganegarei |
| Acropomatiformes | Creediidae | Limnichthys fasciatus | native | Barred sand burrower | Japanese : Tobiginpo |
| Acropomatiformes | Creediidae | Limnichthys nitidus | native | Sand submarine | Japanese : Minami-tobi-ginpo |
| Lophiiformes | Linophrynidae | Linophryne arborifera | native | Japanese : Oni-ankô | |
| Lophiiformes | Linophrynidae | Linophryne densiramus | native | Thickbranch angler | Japanese : Oni-ankō |
| Lophiiformes | Linophrynidae | Linophryne indica | native | Headlight angler | |
| Siluriformes | Amblycipitidae | Liobagrus reinii | native | Japanese : Akaza | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma dorsoluteum | native | Japanese : Futairo-hana suzuki | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma erythraeum | native | Japanese : Benisuzuki | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma japonicum | native | Japanese : Toge-hanasuzuki | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma latifasciatum | native | Blackstripe basslet | Japanese : Tsurugue |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma lunulatum | native | ||
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma maculatum | native | Japanese : Hanasuzuki | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma mitratum | native | Pinstriped basslet | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma pallidum | native | Pallid basslet | |
| Perciformes/Serranoidei | Liopropomatidae | Liopropoma susumi | native | Meteor perch | Japanese : Kosuji-hanasuzuki |
| Pleuronectiformes | Pleuronectidae | Liopsetta pinnifasciata | native | Far Eastern smooth flounder | Japanese : Tôgarei |
| Perciformes/Scorpaenoidei | Setarchidae | Lioscorpius longiceps | native | Slender scorpionfish | Japanese : Yase-akakasago |
| Perciformes/Cottoidei | Liparidae | Liparis agassizii | native | Japanese : Ezo-kusa-uo | |
| Perciformes/Cottoidei | Liparidae | Liparis bikunin | native | Japanese : Ama-kusa-uo | |
| Perciformes/Cottoidei | Liparidae | Liparis burkei | native | Japanese : Nise-soko-shiro | |
| Perciformes/Cottoidei | Liparidae | Liparis curilensis | native | ||
| Perciformes/Cottoidei | Liparidae | Liparis dubius | native | ||
| Perciformes/Cottoidei | Liparidae | Liparis frenatus | native | Japanese : Kanten-bikunin | |
| Perciformes/Cottoidei | Liparidae | Liparis miostomus | native | Japanese : Kokuchi-kusa-uo | |
| Perciformes/Cottoidei | Liparidae | Liparis ochotensis | native | Japanese : Agonashi-kusa-uo | |
| Perciformes/Cottoidei | Liparidae | Liparis owstoni | native | Japanese : Ôsuton-kusa-uo | |
| Perciformes/Cottoidei | Liparidae | Liparis punctulatus | native | Japanese : Aka-bikunin | |
| Perciformes/Cottoidei | Liparidae | Liparis tanakae | native | Tanaka's snailfish | Japanese : Kusa-uo |
| Perciformes/Cottoidei | Liparidae | Liparis tessellatus | native | Japanese : Bikunin | |
| Perciformes/Cottoidei | Liparidae | Lipariscus nanus | native | Pygmy snailfish | Japanese : Kobito-kusa-uo |
| Eupercaria/misc | Lutjanidae | Lipocheilus carnolabrum | native | Tang's snapper | Japanese : Kibire-fuedai |
| Argentiniformes | Bathylagidae | Lipolagus ochotensis | native | Eared blacksmelt | Japanese : Soko-iwashi |
| Myctophiformes | Myctophidae | Lobianchia gemellarii | native | Cocco's lantern fish | Japanese : Hakutô-hadaka |
| Acanthuriformes | Lobotidae | Lobotes surinamensis | native | Tripletail | Japanese : Matsudai |
| Lophiiformes | Lophiidae | Lophiodes endoi | native | Anglerfish | |
| Lophiiformes | Lophiidae | Lophiodes fimbriatus | native | ||
| Lophiiformes | Lophiidae | Lophiodes miacanthus | native | Japanese : Shimofuri-hana-ankô | |
| Lophiiformes | Lophiidae | Lophiodes mutilus | native | Smooth angler | Japanese : Medama-ankô |
| Lophiiformes | Lophiidae | Lophiodes triradiatus | native | Shortspine goosefish | |
| Lophiiformes | Lophiidae | Lophiomus setigerus | native | Blackmouth angler | Japanese : Ki-anko |
| Lophiiformes | Lophiidae | Lophius litulon | native | Yellow goosefish | Japanese : Ki-ankô |
| Lampriformes | Lophotidae | Lophotus capellei | native | Unicornfish | Japanese : Akanamada |
| Gadiformes | Moridae | Lotella phycis | native | Beardie | Japanese : Iso-ainame |
| Gadiformes | Moridae | Lotella tosaensis | native | Japanese : Hosodara | |
| Gobiiformes | Gobiidae | Lotilia klausewitzi | native | Dancer shrimp goby | Japanese : Odori-haze; Japanese : Odorihaze; |
| Myctophiformes | Myctophidae | Loweina terminata | native | Japanese : Kirara-hadaka | |
| Carcharhiniformes | Carcharhinidae | Loxodon macrorhinus | native | Sliteye shark | Japanese : Togarimezame |
| Ovalentaria/misc | Pseudochromidae | Lubbockichthys tanakai | native | Tanaka's dottyback | |
| Gobiiformes | Gobiidae | Lubricogobius dinah | native | Dinah's goby | Japanese : Nakamoto-irowake-haze |
| Gobiiformes | Gobiidae | Lubricogobius exiguus | native | Japanese : Mijinbenihaze | |
| Gobiiformes | Gobiidae | Lubricogobius ornatus | native | Ornate slippery goby | Japanese : Irezumi-mijn-benihaze |
| Ophidiiformes | Ophidiidae | Luciobrotula bartschi | native | Japanese : Kuro-umidojô | |
| Gobiiformes | Gobiidae | Luciogobius adapel | native | Japanese : Kawari-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius albus | endemic | Japanese : Dôkutsu-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius ama | native | ||
| Gobiiformes | Gobiidae | Luciogobius dormitoris | native | Japanese : Nemuri-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius elongatus | native | Japanese : Naga-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius fluvialis | native | Japanese : Nagare-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius fonticola | native | Japanese : Yusui-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius grandis | native | Japanese : Ô-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius guttatus | native | Flat-headed goby | Japanese : Mimizuhaze |
| Gobiiformes | Gobiidae | Luciogobius koma | native | Japanese : Komahaze | |
| Gobiiformes | Gobiidae | Luciogobius pallidus | endemic | Japanese : Ido-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius parvulus | native | Japanese : Nansenhaze | |
| Gobiiformes | Gobiidae | Luciogobius platycephalus | native | Japanese : Yari-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius ryukyuensis | native | Japanese : Minami-hime-mimizuhaze | |
| Gobiiformes | Gobiidae | Luciogobius saikaiensis | native | Japanese : Hige-mimizuhaze | |
| Perciformes/Zoarcoidei | Lumpenidae | Lumpenella longirostris | native | Longsnout prickleback | Japanese : Nezumiginpo |
| Perciformes/Zoarcoidei | Opisthocentridae | Lumpenopsis pavlenkoi | native | Japanese : Tongariginpo | |
| Perciformes/Zoarcoidei | Opisthocentridae | Lumpenopsis triocellata | native | Japanese : Mitsuboshiginpo | |
| Perciformes/Zoarcoidei | Lumpenidae | Lumpenus sagitta | native | Snake prickleback | Japanese : Unagigaji |
| Gobiiformes | Gobiidae | Luposicya lupus | native | Wolfsnout goby | Japanese : Yagihaze |
| Eupercaria/misc | Lutjanidae | Lutjanus argentimaculatus | native | Mangrove red snapper | Japanese : Goma-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus bengalensis | native | Bengal snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus bohar | native | Two-spot red snapper | Japanese : Bara-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus boutton | native | Moluccan snapper | Japanese : Kyûssen-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus decussatus | native | Checkered snapper | Japanese : Amime-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus dodecacanthoides | native | Sunbeam snapper | Japanese : Kisuji-tarumi |
| Eupercaria/misc | Lutjanidae | Lutjanus ehrenbergii | native | Blackspot snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus erythropterus | native | Crimson snapper | Japanese : Yoko-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus fulviflamma | native | Dory snapper | Japanese : Nisekurohoshi-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus fulvus | native | Blacktail snapper | Japanese : Oki-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus gibbus | native | Humpback red snapper | Japanese : Hime-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus johnii | native | John's snapper | Japanese : Minami-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus kasmira | native | Common bluestripe snapper | Japanese : Yosuji-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus lutjanus | native | Bigeye snapper | Japanese : Kinsen-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus malabaricus | native | Malabar blood snapper | Japanese : Yoko-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus monostigma | native | One-spot snapper | Japanese : Itten-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus ophuysenii | native | Spotstripe snapper | Japanese : Yokosuji-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus quinquelineatus | native | Five-lined snapper | Japanese : Rokusen-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus rivulatus | native | Blubberlip snapper | Japanese : Nami-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus rufolineatus | native | Yellow-lined snapper | |
| Eupercaria/misc | Lutjanidae | Lutjanus russellii | native | Russell's snapper | Japanese : Kurohoshi-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus sebae | native | Emperor red snapper | Japanese : Sen-nendai |
| Eupercaria/misc | Lutjanidae | Lutjanus stellatus | native | Star snapper | Japanese : Fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus timoriensis | native | Timor snapper | Japanese : Wakiguro-akafuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus vitta | native | Brownstripe red snapper | Japanese : Yokosuji-fuedai |
| Eupercaria/misc | Lutjanidae | Lutjanus xanthopinnis | native | Yellowfin snapper | Japanese : Imoto-fuedai |
| Acanthuriformes | Luvaridae | Luvarus imperialis | native | Luvar | Japanese : Amashiira |
| Perciformes/Serranoidei | Anthiadidae | Luzonichthys waitei | native | Waite's splitfin | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys albomaculata | native | Japanese : Shirobuchi-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys aurantiaca | native | Japanese : Daidai-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys hippopotamus | native | Japanese : Hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys maculata | native | Japanese : Kurobuchihebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys makushok | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys melanostomias | native | Japanese : Ohôtsuku-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys rassi | native | Japanese : Rasu-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys remissaria | native | Shifted wolf eelpout | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys ryukyuensis | native | Japanese : Ryukyu-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys squamosa | native | Japanese : Uroko-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycenchelys tohokuensis | native | Japanese : Kitagawa-hebigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodapus microchir | native | Japanese : Ashinashigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes albonotatus | native | Japanese : Hanagengi | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes brunneofasciatus | native | Tawnystripe eelpout | Japanese : Harasujigenge |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes caudimaculatus | native | Japanese : Irezumigaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes fasciatus | native | Banded eelpout | Japanese : Ohôtsuku-hakusengaji |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes hubbsi | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes japonicus | native | Japanese : Ashinagagenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes jenseni | native | Japanese : Ebisugaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes macrolepis | native | Japanese : Yokoshimagaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes matsubarai | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes microporus | native | Japanese : Yasemayugaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes mucosus | native | Saddled eelpout | Japanese : Nise-waijigenge |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes nakamurae | native | Japanese : Kurogenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes nishimurai | native | Japanese : Orochigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes obscurus | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes ocellatus | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes paucilepidotus | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes pectoralis | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes sadoensis | native | Japanese : Sado-hinagenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes schmidti | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes sigmatoides | native | Japanese : Esujigaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes soldatovi | native | Japanese : Kurogaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes tanakae | native | Japanese : Tanakagenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes teraoi | native | Japanese : Hinagenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes toyamensis | native | Japanese : Agogenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes uschakovi | native | Japanese : Kawarigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes yamatoi | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Lycodes ygreknotatus | native | Japanese : Waijigenge | |
| Perciformes/Zoarcoidei | Zoarcidae | Lycozoarces regani | native | Japanese : Sedakagenge | |
| Perciformes/Scorpaenoidei | Setarchidae | Lythrichthys cypho | native | Dwarf red deepwater scorpionfsh | Japanese : Azukikasago |
| Perciformes/Scorpaenoidei | Setarchidae | Lythrichthys eulabes | native | Jordan's red deepwater scorpionfsh | Japanese : Akakasago |
| Perciformes/Scorpaenoidei | Setarchidae | Lythrichthys longimanus | native | Red deepwater scorpionfish | Japanese : Sumikui-akakasago |
| Eupercaria/misc | Lutjanidae | Macolor macularis | native | Midnight snapper | |
| Eupercaria/misc | Lutjanidae | Macolor niger | native | Black and white snapper | Japanese : Madaratarumi |
| Gobiiformes | Gobiidae | Macrodontogobius wilburi | native | Largetooth goby | Japanese : Madarahaze |
| Eupercaria/misc | Labridae | Macropharyngodon meleagris | native | Blackspotted wrasse | Japanese : Nodoguro-bera |
| Eupercaria/misc | Labridae | Macropharyngodon moyeri | native | Japanese : Usuba-nodogurobera | |
| Eupercaria/misc | Labridae | Macropharyngodon negrosensis | native | Yellowspotted wrasse | Japanese : Sejiro-nodogurobera |
| Argentiniformes | Opisthoproctidae | Macropinna microstoma | native | Barreleye | Japanese : Demenigisu |
| Anabantiformes | Osphronemidae | Macropodus ocellatus | native | Round tail paradisefish | Japanese : Chôsen-buna |
| Anabantiformes | Osphronemidae | Macropodus opercularis | native | Paradisefish | Japanese : Taiwan-kingyo |
| Syngnathiformes | Centriscidae | Macroramphosus scolopax | native | Longspine snipefish | Japanese : Sagifue |
| Tetraodontiformes | Triacanthodidae | Macrorhamphosodes uradoi | native | Trumpetsnout | Japanese : Fuekawamuki |
| Aulopiformes | Paralepididae | Magnisudis atlantica | native | Duckbill barracudina | Japanese : Kusabi-uroko-eso |
| Aulopiformes | Paralepididae | Magnisudis indica | native | Japanese : Indo-kusabi-uroko-eso | |
| Gobiiformes | Gobiidae | Mahidolia mystacina | native | Flagfin prawn goby | Japanese : Kasurihaze |
| Carangiformes | Istiophoridae | Makaira mazara | native | Indo-Pacific blue marlin | Japanese : Tsun |
| Eupercaria/misc | Malacanthidae | Malacanthus brevirostris | native | Quakerfish | Japanese : Yase-amadai |
| Eupercaria/misc | Malacanthidae | Malacanthus latovittatus | native | Blue blanquillo | Japanese : Kitsune-amadai |
| Gadiformes | Macrouridae | Malacocephalus nipponensis | native | Japanese : Nihon-manjudara | |
| Perciformes/Cottoidei | Psychrolutidae | Malacocottus aleuticus | native | Whitetail sculpin | |
| Perciformes/Cottoidei | Psychrolutidae | Malacocottus gibber | native | Japanese : Sepparikajika | |
| Perciformes/Cottoidei | Psychrolutidae | Malacocottus kincaidi | native | Blackfin sculpin | |
| Perciformes/Cottoidei | Psychrolutidae | Malacocottus zonurus | native | Darkfin sculpin | Japanese : Kobushikajika |
| Stomiiformes | Stomiidae | Malacosteus niger | native | Stoplight loosejaw | Japanese : Ôkuchi-hoshi-eso |
| Acropomatiformes | Malakichthyidae | Malakichthys barbatus | native | Japanese : Hige-ômehata | |
| Acropomatiformes | Malakichthyidae | Malakichthys elegans | native | Splendid seabass | Japanese : Naga-ômehata |
| Acropomatiformes | Malakichthyidae | Malakichthys griseus | native | Japanese : ômehata | |
| Acropomatiformes | Malakichthyidae | Malakichthys wakiyae | native | Japanese : Wakiyahata | |
| Osmeriformes | Osmeridae | Mallotus villosus | native | Capelin | Japanese : Karafuto-shishamo |
| Lophiiformes | Ogcocephalidae | Malthopsis annulifera | native | Ring triangular batfish | Japanese : Wanuke-fûryû-uo |
| Lophiiformes | Ogcocephalidae | Malthopsis gigas | native | Giant triangular batfish | Japanese : Kowanuke-furyuuo |
| Lophiiformes | Ogcocephalidae | Malthopsis kobayashii | native | Kobayashi's triangular batfish | |
| Lophiiformes | Ogcocephalidae | Malthopsis mitrigera | native | Two-spine triangular batfish | Japanese : Kagi-fûryû-uo |
| Lophiiformes | Ogcocephalidae | Malthopsis tiarella | native | Spearnose seabat | Japanese : Goma-fûryû-uo |
| Gobiiformes | Gobiidae | Mangarinus waterousi | native | Japanese : Uchiwahaze | |
| Stomiiformes | Gonostomatidae | Margrethia obtusirostra | native | Bighead portholefish | Japanese : Renju-eso |
| Syngnathiformes | Syngnathidae | Maroubra yasudai | native | Orange pipefish | Japanese : Daidai-yôji |
| Perciformes/Cottoidei | Rhamphocottidae | Marukawichthys ambulator | native | Japanese : Marukawakajika | |
| Tetraodontiformes | Molidae | Masturus lanceolatus | native | Sharptail mola | Japanese : Tongari-yarimanbô; Japanese : Yarimanbô; |
| Acropomatiformes | Hemerocoetidae | Matsubaraea fusiformis | native | ||
| Alepocephaliformes | Platytroctidae | Maulisia acuticeps | native | Sharpsnout tubeshoulder | |
| Stomiiformes | Sternoptychidae | Maurolicus japonicus | native | North Pacific lightfish | Japanese : Kyūri-eso |
| Stomiiformes | Sternoptychidae | Maurolicus muelleri | native | Silvery lightfish | Japanese : Kyuurieso |
| Anguilliformes | Synaphobranchidae | Meadia abyssalis | native | Abyssal cutthroat eel | Japanese : Hirejiro-anago |
| Lamniformes | Megachasmidae | Megachasma pelagios | native | Megamouth shark | |
| Carangiformes | Carangidae | Megalaspis cordyla | native | Torpedo scad | Japanese : Oni-aji |
| Cypriniformes | Xenocyprididae | Megalobrama amblycephala | introduced | Wuchang bream | |
| Eupercaria/misc | Sciaenidae | Megalonibea fusca | native | Japanese : Shina-ô-nibe | |
| Elopiformes | Megalopidae | Megalops cyprinoides | native | Indo-Pacific tarpon | Japanese : Isegoi |
| Perciformes/Serranoidei | Anthiadidae | Meganthias kingyo | native | ||
| Blenniiformes | Blenniidae | Meiacanthus atrodorsalis | native | Forktail blenny | |
| Blenniiformes | Blenniidae | Meiacanthus ditrema | native | One-striped poison-fang blenny | Japanese : Satsukiginpo |
| Blenniiformes | Blenniidae | Meiacanthus grammistes | native | Striped poison-fang blenny | Japanese : Hige-nijiginpo |
| Blenniiformes | Blenniidae | Meiacanthus kamoharai | native | Japanese : Kamoharaginpo | |
| Beryciformes | Melamphaidae | Melamphaes longivelis | native | Eyebrow bigscale | Japanese : Maru-kabuto-uo |
| Beryciformes | Melamphaidae | Melamphaes lugubris | native | Highsnout melamphid | Japanese : Hon-kabuto-uo |
| Beryciformes | Melamphaidae | Melamphaes polylepis | native | Japanese : Uroko-kabuto-uo | |
| Beryciformes | Melamphaidae | Melamphaes proximus | native | ||
| Lophiiformes | Melanocetidae | Melanocetus johnsonii | native | Humpback anglerfish | Japanese : Perikan-ankô |
| Argentiniformes | Bathylagidae | Melanolagus bericoides | native | Bigscale deepsea smelt | Japanese : Nettai soko iwashi |
| Perciformes/Zoarcoidei | Zoarcidae | Melanostigma orientale | native | Japanese : Konnyakuhadakagenge | |
| Stomiiformes | Stomiidae | Melanostomias melanops | native | Japanese : Shirohige-hoshi-eso | |
| Stomiiformes | Stomiidae | Melanostomias paucilaternatus | native | Spothead dragonfish | Japanese : Kanten-hoshi-eso |
| Stomiiformes | Stomiidae | Melanostomias pauciradius | native | Three-ray dragonfish | Japanese : Kanten-tokagegisu |
| Stomiiformes | Stomiidae | Melanostomias pollicifer | native | Japanese : Namida-hoshi-eso | |
| Stomiiformes | Stomiidae | Melanostomias tentaculatus | native | Tentacle dragonfish | Japanese : Kurohige-hoshi-eso |
| Stomiiformes | Stomiidae | Melanostomias valdiviae | native | Valdivia black dragon fish | Japanese : Barudibia-hoshi-eso |
| Tetraodontiformes | Balistidae | Melichthys niger | native | Black triggerfish | Japanese : Soroimongara |
| Tetraodontiformes | Balistidae | Melichthys vidua | native | Pinktail triggerfish | Japanese : Kuromongara |
| Carangaria/misc | Menidae | Mene maculata | native | Moonfish | Japanese : Ginkagami |
| Gadiformes | Merlucciidae | Merluccius tasmanicus | native | ||
| Centrarchiformes | Terapontidae | Mesopristes argenteus | native | Silver grunter | Japanese : Nise-shima-isaki |
| Centrarchiformes | Terapontidae | Mesopristes cancellatus | native | Tapiroid grunter | Japanese : Yokoshima-isaki |
| Centrarchiformes | Terapontidae | Mesopristes iravi | native | Japanese : Shimizu-shimaisaki | |
| Lampriformes | Veliferidae | Metavelifer multiradiatus | native | Spinyfin velifer | Japanese : Hime-kusa-aji |
| Centrarchiformes | Microcanthidae | Microcanthus strigatus | native | Stripey | Japanese : Kagokakidai |
| Perciformes/Cottoidei | Cottidae | Microcottus sellaris | native | Brightbelly sculpin | Japanese : Ohotsukutsunokajika |
| Syngnathiformes | Syngnathidae | Micrognathus andersonii | native | Shortnose pipefish | Japanese : Kanmuri-yôji |
| Lophiiformes | Oneirodidae | Microlophichthys microlophus | native | Short-rod anglerfish | |
| Gobiiformes | Odontobutidae | Micropercops cinctus | native | ||
| Gobiiformes | Odontobutidae | Micropercops swinhonis | native | ||
| Syngnathiformes | Syngnathidae | Microphis brachyurus | native | Short-tailed pipefish | Japanese : Tengu-yôji |
| Syngnathiformes | Syngnathidae | Microphis leiaspis | native | Barhead pipefish | Japanese : Issen-yôji |
| Syngnathiformes | Syngnathidae | Microphis millepunctatus | native | Shorttail pipefish | |
| Centrarchiformes | Centrarchidae | Micropterus dolomieu | introduced | Smallmouth bass | Japanese : Kokuchibasu |
| Centrarchiformes | Centrarchidae | Micropterus salmoides | introduced | Largemouth black bass | Japanese : Okuchibasu |
| Pleuronectiformes | Pleuronectidae | Microstomus achne | native | Slime flounder | Japanese : Babagarei |
| Pleuronectiformes | Pleuronectidae | Microstomus bathybius | native | Deep-sea sole | Japanese : Shimofurigarei |
| Eupercaria/misc | Sciaenidae | Miichthys miiuy | native | Mi-iuy croaker | Japanese : Hon-nibe |
| Blenniiformes | Blenniidae | Mimoblennius atrocinctus | native | Spotted and barred blenny | Japanese : Matsubaginpo |
| Perciformes/Scorpaenoidei | Synanceiidae | Minous groeneveldi | native | Groeneveld's stingfish | |
| Perciformes/Scorpaenoidei | Synanceiidae | Minous monodactylus | native | Grey stingfish | Japanese : Hime-okoze |
| Perciformes/Scorpaenoidei | Synanceiidae | Minous pusillus | native | Dwarf stingfish | Japanese : Yase-okoze |
| Perciformes/Scorpaenoidei | Synanceiidae | Minous quincarinatus | native | Japanese : Ito-okoze | |
| Gobiiformes | Gobiidae | Minysicya caudimaculata | native | Blackspot minigoby | |
| Perciformes/Serranoidei | Anthiadidae | Mirolabrichthys pascalus | native | Amethyst anthias | Japanese : Hanagoi |
| Perciformes/Serranoidei | Anthiadidae | Mirolabrichthys tuka | native | Yellowstriped fairy basslet | |
| Cypriniformes | Cobitidae | Misgurnus anguillicaudatus | native | Pond loach | Japanese : Dojô |
| Cypriniformes | Cobitidae | Misgurnus dabryanus | introduced | ||
| Cypriniformes | Cobitidae | Misgurnus mizolepis | native | Chinese muddy loach | |
| Lamniformes | Mitsukurinidae | Mitsukurina owstoni | native | Goblin shark | Japanese : Teguzame |
| Myliobatiformes | Mobulidae | Mobula alfredi | native | Reef manta ray | Japanese : Riifu Oniitomakiei |
| Myliobatiformes | Mobulidae | Mobula birostris | native | Oceanic manta ray | Japanese : Oni-itomaki-ei |
| Myliobatiformes | Mobulidae | Mobula mobular | native | Spinetail devil ray | Japanese : Itomaki-ei |
| Myliobatiformes | Mobulidae | Mobula tarapacana | native | Sicklefin devil ray | |
| Tetraodontiformes | Molidae | Mola alexandrini | native | Bumphead sunfish | Japanese : Ushi-manbo |
| Tetraodontiformes | Molidae | Mola mola | native | Ocean sunfish | Japanese : Manbô |
| Tetraodontiformes | Monacanthidae | Monacanthus chinensis | native | Fan-bellied leatherjacket | Japanese : Morokoshihagi |
| Trachichthyiformes | Monocentridae | Monocentris chrysadamas | native | Golden-diamond pineapple fish | |
| Trachichthyiformes | Monocentridae | Monocentris japonica | native | Pineconefish | Japanese : Matsukasa-uo |
| Eupercaria/misc | Monodactylidae | Monodactylus argenteus | native | Silver moony | Japanese : Himetsubameuo |
| Saccopharyngiformes | Monognathidae | Monognathus isaacsi | native | ||
| Ophidiiformes | Ophidiidae | Monomitopus kumae | native | Japanese : Kuma-itachiuo | |
| Ophidiiformes | Ophidiidae | Monomitopus pallidus | native | Japanese : Yaeba-kuma-itachiuo | |
| Synbranchiformes | Synbranchidae | Monopterus albus | native | Asian swamp eel | Japanese : Ta-unagi |
| Eupercaria/misc | Lethrinidae | Monotaxis grandoculis | native | Humpnose big-eye bream | Japanese : Yokoshima-kurodai |
| Mugiliformes | Mugilidae | Moolgarda buchanani | native | Bluetail mullet | Japanese : Kamahire-bora |
| Mugiliformes | Mugilidae | Moolgarda crenilabis | native | Fringelip mullet | Japanese : Fûrai-bora |
| Mugiliformes | Mugilidae | Moolgarda heterocheilos | native | Half fringelip mullet | Japanese : Nagare-fûrai-bora |
| Mugiliformes | Mugilidae | Moolgarda pedaraki | native | Longfin mullet | |
| Mugiliformes | Mugilidae | Moolgarda seheli | native | Bluespot mullet | Japanese : Taiwan-menada |
| Anguilliformes | Moringuidae | Moringua abbreviata | native | Japanese : Harigane-umihebi | |
| Anguilliformes | Moringuidae | Moringua bicolor | native | Bicolor spaghetti eel | |
| Anguilliformes | Moringuidae | Moringua ferruginea | native | Rusty spaghetti eel | |
| Anguilliformes | Moringuidae | Moringua javanica | native | Java spaghetti eel | Japanese : Tobi-harigane-umihebi |
| Anguilliformes | Moringuidae | Moringua microchir | native | Lesser thrush eel | |
| Mugiliformes | Mugilidae | Mugil cephalus | native | Flathead grey mullet | Japanese : Bora |
| Gobiiformes | Gobiidae | Mugilogobius abei | native | Japanese : Abehaze | |
| Gobiiformes | Gobiidae | Mugilogobius cavifrons | native | Japanese : Kumahaze | |
| Gobiiformes | Gobiidae | Mugilogobius chulae | native | Yellowstripe goby | Japanese : Namihaze |
| Gobiiformes | Gobiidae | Mugilogobius fuscus | native | Japanese : Futahoshihaze | |
| Gobiiformes | Gobiidae | Mugilogobius mertoni | native | Chequered mangrove goby | |
| Gobiiformes | Gobiidae | Mugilogobius notospilus | native | Freshwater mangrovegoby | Japanese : Izumihaze |
| Gobiiformes | Gobiidae | Mugilogobius tagala | native | Japanese : Hohogurohaze | |
| Mulliformes | Mullidae | Mulloidichthys flavolineatus | native | Yellowstripe goatfish | Japanese : Montsuki-akahimeji |
| Mulliformes | Mullidae | Mulloidichthys pfluegeri | native | Pflueger's goatfish | Japanese : Ryukyu-akahimeji |
| Mulliformes | Mullidae | Mulloidichthys vanicolensis | native | Yellowfin goatfish | Japanese : Akahimeji |
| Anguilliformes | Muraenesocidae | Muraenesox bagio | native | Common pike conger | Japanese : Suzu-hamo |
| Anguilliformes | Muraenesocidae | Muraenesox cinereus | native | Daggertooth pike conger | Japanese : Hamo |
| Anguilliformes | Muraenesocidae | Muraenesox yamaguchiensis | native | ||
| Anguilliformes | Ophichthidae | Muraenichthys gymnopterus | native | Japanese : Wakaunagi | |
| Anguilliformes | Ophichthidae | Muraenichthys schultzei | native | Maimed snake eel | Japanese : Minami-mimizu-anago |
| Carcharhiniformes | Triakidae | Mustelus griseus | native | Spotless smooth-hound | Japanese : Shirozame |
| Carcharhiniformes | Triakidae | Mustelus manazo | native | Starspotted smooth-hound | Japanese : Hoshizame |
| Myctophiformes | Myctophidae | Myctophum aurolaternatum | native | Golden lanternfish | Japanese : Hikari-hadaka |
| Myctophiformes | Myctophidae | Myctophum nitidulum | native | Pearly lanternfish | Japanese : Susuki-hadaka |
| Myctophiformes | Myctophidae | Myctophum orientale | native | Oriental lanternfish | Japanese : Usu-hadaka |
| Gobiiformes | Gobiidae | Myersina filifer | native | Filamentous shrimpgoby | Japanese : Itohikihaze |
| Gobiiformes | Gobiidae | Myersina macrostoma | native | Bigmouth shrimpgoby | Japanese : Hagoromohaze |
| Gobiiformes | Gobiidae | Myersina nigrivirgata | native | Black-line shrimp-goby | Japanese : Kuro-obihaze |
| Myliobatiformes | Myliobatidae | Myliobatis hamlyni | native | Purple eagle ray | |
| Myliobatiformes | Myliobatidae | Myliobatis tobijei | native | Japanese eagle ray | Japanese : Tobi-ei |
| Cypriniformes | Xenocyprididae | Mylopharyngodon piceus | introduced | Black carp | Japanese : Ao-uo |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus brandtii | native | Japanese : Shimofurikajika | |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus jaok | native | Plain sculpin | Japanese : Okukajika |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus matsubarai | native | Japanese : Togarikajika | |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus polyacanthocephalus | native | Great sculpin | Japanese : Togekajika |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus stelleri | native | Steller's sculpin | Japanese : Gisukajika; Japanese : Samekajika; |
| Perciformes/Cottoidei | Cottidae | Myoxocephalus yesoensis | native | ||
| Anguilliformes | Ophichthidae | Myrichthys colubrinus | native | Harlequin snake eel | Japanese : Shima-umihebi |
| Anguilliformes | Ophichthidae | Myrichthys maculosus | native | Tiger snake eel | Japanese : Moyô-mongaradôshi |
| Holocentriformes | Holocentridae | Myripristis adusta | native | Shadowfin soldierfish | Japanese : Tsumaguro-matsukasa |
| Holocentriformes | Holocentridae | Myripristis amaena | native | Brick soldierfish | Japanese : Ame-matsukasa |
| Holocentriformes | Holocentridae | Myripristis berndti | native | Blotcheye soldierfish | Japanese : Akamatsukasa |
| Holocentriformes | Holocentridae | Myripristis botche | native | Blacktip soldierfish | Japanese : Uroko-matsukasa |
| Holocentriformes | Holocentridae | Myripristis chryseres | native | Yellowfin soldierfish | Japanese : Kibire-matsukasa |
| Holocentriformes | Holocentridae | Myripristis greenfieldi | native | ||
| Holocentriformes | Holocentridae | Myripristis hexagona | native | Doubletooth soldierfish | Japanese : Maru-matsukasa |
| Holocentriformes | Holocentridae | Myripristis kochiensis | native | ||
| Holocentriformes | Holocentridae | Myripristis kuntee | native | Shoulderbar soldierfish | Japanese : Kuro-obi-matsukasa |
| Holocentriformes | Holocentridae | Myripristis murdjan | native | Pinecone soldierfish | Japanese : Yogore-matsukasa |
| Holocentriformes | Holocentridae | Myripristis pralinia | native | Scarlet soldierfish | Japanese : Kogane-matsukasa |
| Holocentriformes | Holocentridae | Myripristis violacea | native | Lattice soldierfish | |
| Holocentriformes | Holocentridae | Myripristis vittata | native | Whitetip soldierfish | Japanese : Beni-matsukasa |
| Holocentriformes | Holocentridae | Myripristis woodsi | native | Whitespot soldierfish | |
| Anguilliformes | Ophichthidae | Myrophis microchir | native | Ordinary snake eel | Japanese : Serebesu-hire-anago |
| Myxiniformes | Myxinidae | Myxine garmani | native | Japanese : Mekura-unagi | |
| Myxiniformes | Myxinidae | Myxine paucidens | native | ||
| Pleuronectiformes | Pleuronectidae | Myzopsetta proboscidea | native | Longhead dab | Japanese : Hanagarei |
| Pleuronectiformes | Pleuronectidae | Myzopsetta punctatissima | native | Dotted flounder | Japanese : Sunagarei |
| Blenniiformes | Blenniidae | Nannosalarias nativitatis | native | Pygmy blenny | Japanese : Hinaginpo |
| Argentiniformes | Microstomatidae | Nansenia ahlstromi | native | ||
| Argentiniformes | Microstomatidae | Nansenia ardesiaca | native | Robust smallmouth | Japanese : Ginzake-iwashi |
| Argentiniformes | Microstomatidae | Nansenia candida | native | Bluethroat argentine | Japanese : Kurosake-iwashi |
| Alepocephaliformes | Alepocephalidae | Narcetes kamoharai | native | Japanese : Kuromasuku-iwashi | |
| Alepocephaliformes | Alepocephalidae | Narcetes shonanmaruae | native | Yokozuna Slickhead | Japanese : Yokozuna iwashi |
| Alepocephaliformes | Alepocephalidae | Narcetes wonderi | native | ||
| Torpediniformes | Narcinidae | Narcine timlei | native | Spotted numbfish | Japanese : Taiwan-shibire-ei; Japanese : Yaito Shibireei; |
| Torpediniformes | Narkidae | Narke dipterygia | native | Numbray | Japanese : Hakuten-shibire-ei |
| Torpediniformes | Narkidae | Narke japonica | native | Japanese sleeper ray | Japanese : Shibire-ei |
| Acanthuriformes | Acanthuridae | Naso annulatus | native | Whitemargin unicornfish | Japanese : Hime-tenguhagi |
| Acanthuriformes | Acanthuridae | Naso brachycentron | native | Humpback unicornfish | Japanese : Oni-tenguhagi |
| Acanthuriformes | Acanthuridae | Naso brevirostris | native | Spotted unicornfish | Japanese : Tsumari-tenguhagi |
| Acanthuriformes | Acanthuridae | Naso fageni | native | Horseface unicornfish | Japanese : Moai-tenguhagi |
| Acanthuriformes | Acanthuridae | Naso hexacanthus | native | Sleek unicornfish | Japanese : Tenguhagi-modoki |
| Acanthuriformes | Acanthuridae | Naso lituratus | native | Orangespine unicornfish | Japanese : Miyako-tenguhagi |
| Acanthuriformes | Acanthuridae | Naso lopezi | native | Elongate unicornfish | Japanese : Naga-tenguhagi-modoki |
| Acanthuriformes | Acanthuridae | Naso maculatus | native | Scribbled unicornfish | Japanese : Goma-tenguhagi-modoki |
| Acanthuriformes | Acanthuridae | Naso tergus | native | Japanese : Shinobi-tenguhagi | |
| Acanthuriformes | Acanthuridae | Naso thynnoides | native | Oneknife unicornfish | Japanese : Bôzuhagi |
| Acanthuriformes | Acanthuridae | Naso tonganus | native | Bulbnose unicornfish | Japanese : Tosakahagi |
| Acanthuriformes | Acanthuridae | Naso unicornis | native | Bluespine unicornfish | Japanese : Tenguhagi |
| Acanthuriformes | Acanthuridae | Naso vlamingii | native | Bignose unicornfish | Japanese : Sazanami-tosakahagi |
| Carangiformes | Carangidae | Naucrates ductor | native | Pilotfish | Japanese : Burimodoki |
| Perciformes/Cottoidei | Agonidae | Nautichthys pribilovius | native | Eyeshade sculpin | Japanese : Okozekajika |
| Gobiiformes | Microdesmidae | Navigobius asayake | native | Sunrise dartfish | Japanese : Asayake-kaguya-haze |
| Gobiiformes | Microdesmidae | Navigobius dewa | native | ||
| Scombriformes | Gempylidae | Nealotus tripes | native | Black snake mackerel | Japanese : Fûraikamasu |
| Kurtiformes | Apogonidae | Neamia octospina | native | Eightspine cardinalfish | Japanese : Yatsutoge-tenjikudai |
| Orectolobiformes | Ginglymostomatidae | Nebrius ferrugineus | native | Tawny nurse shark | Japanese : Ô-tenjikuzame |
| Kurtiformes | Apogonidae | Nectamia bandanensis | native | Bigeye cardinalfish | Japanese : Banda-ishimochi |
| Kurtiformes | Apogonidae | Nectamia fusca | native | Ghost cardinalfish | Japanese : Hososuji-namida-tenjikudai; Japanese : Oguro-tenjikudai; |
| Kurtiformes | Apogonidae | Nectamia savayensis | native | Samoan cardinalfish | Japanese : Namida-tenjikudai |
| Perciformes/Cottoidei | Liparidae | Nectoliparis pelagicus | native | Tadpole snailfish | Japanese : Kanten-uo |
| Anguilliformes | Ophichthidae | Neenchelys mccoskeri | native | McCosker's worm eel | Japanese : Tsurugi-mukashi-umihebi |
| Anguilliformes | Ophichthidae | Neenchelys similis | native | Slender work eel | |
| Carcharhiniformes | Carcharhinidae | Negaprion acutidens | native | Sicklefin lemon shark | Japanese : Remonzame |
| Perciformes/Serranoidei | Anthiadidae | Nemanthias bicolor | native | Bicolor anthias | Japanese : Futairo-hanagoi |
| Perciformes/Serranoidei | Anthiadidae | Nemanthias dispar | native | Peach fairy basslet | Japanese : Akane-hanagoi |
| Clupeiformes | Dorosomatidae | Nematalosa japonica | native | Japanese gizzard shad | Japanese : Dorokui |
| Clupeiformes | Dorosomatidae | Nematalosa nasus | native | Bloch's gizzard shad | |
| Gobiiformes | Microdesmidae | Nemateleotris decora | native | Elegant firefish | Japanese : Akebonohaze |
| Gobiiformes | Microdesmidae | Nemateleotris lavandula | native | Lavender-blushed dartfish | |
| Gobiiformes | Microdesmidae | Nemateleotris magnifica | native | Fire goby | Japanese : Hatatatehaze |
| Anguilliformes | Nemichthyidae | Nemichthys scolopaceus | native | Slender snipe eel | Japanese : Shigi-unagi |
| Eupercaria/misc | Nemipteridae | Nemipterus aurora | native | Dawn threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus bathybius | native | Yellowbelly threadfin bream | Japanese : Soko-itoyori |
| Eupercaria/misc | Nemipteridae | Nemipterus furcosus | native | Forktail threadfin bream | Japanese : Momo-itoyori |
| Eupercaria/misc | Nemipteridae | Nemipterus hexodon | native | Ornate threadfin bream | Japanese : Niji-Itoyori |
| Eupercaria/misc | Nemipteridae | Nemipterus japonicus | native | Japanese threadfin bream | Japanese : Nihon-itoyori |
| Eupercaria/misc | Nemipteridae | Nemipterus thosaporni | native | Palefin threadfin bream | |
| Eupercaria/misc | Nemipteridae | Nemipterus virgatus | native | Golden threadfin bream | Japanese : Itoyoridai |
| Eupercaria/misc | Nemipteridae | Nemipterus zysron | native | Slender threadfin bream | Japanese : Hime-itoyori |
| Acropomatiformes | Bathyclupeidae | Neobathyclupea japanotaiwana | native | North Pacific deepsea herring | |
| Ophidiiformes | Ophidiidae | Neobythites australiensis | native | Australian cusk | Japanese : Niten-itachiuo |
| Ophidiiformes | Ophidiidae | Neobythites machidai | native | Japanese : Machida-itachiuo | |
| Ophidiiformes | Ophidiidae | Neobythites sivicola | native | Japanese : Shio-itachiuo | |
| Ophidiiformes | Ophidiidae | Neobythites stigmosus | native | Japanese : Shima-stigmosus | |
| Ophidiiformes | Ophidiidae | Neobythites unimaculatus | native | Onespot cusk | Japanese : Sumitsuki-itachiuo |
| Perciformes/Scorpaenoidei | Tetrarogidae | Neocentropogon japonicus | native | Japanese : Naga-hachi-okoze | |
| Centrarchiformes | Cirrhitidae | Neocirrhites armatus | native | Flame hawkfish | Japanese : Benigonbe |
| Blenniiformes | Chaenopsidae | Neoclinus bryope | native | Japanese : Koke-ginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus chihiroe | native | Japanese : Shizumiiso-koke-ginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus lacunicola | native | Japanese : Iwa-ana-kokeginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus monogrammus | native | Japanese : Chishio-kokeginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus nudiceps | native | Japanese : Oki-matsuge | |
| Blenniiformes | Chaenopsidae | Neoclinus nudus | native | Japanese : Hadaka-koke-ginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus okazakii | native | Japanese : Araiso-koke-ginpo | |
| Blenniiformes | Chaenopsidae | Neoclinus toshimaensis | native | Japanese : Toshima-kokeginpo | |
| Ovalentaria/misc | Embiotocidae | Neoditrema ransonnetii | native | Japanese : Okitango | |
| Scombriformes | Gempylidae | Neoepinnula minetomai | native | Large-eyed sackfish | Japanese : Erabu-sumiyaki |
| Scombriformes | Gempylidae | Neoepinnula orientalis | native | Sackfish | Japanese : Sokosumiyaki |
| Ovalentaria/misc | Pomacentridae | Neoglyphidodon melas | native | Bowtie damselfish | Japanese : Kuro-suzumedai |
| Ovalentaria/misc | Pomacentridae | Neoglyphidodon nigroris | native | Black-and-gold chromis | Japanese : Hirenaga-suzumedai |
| Pleuronectiformes | Bothidae | Neolaeops microphthalmus | native | Crosseyed flounder | Japanese : Semushidarumagarei |
| Perciformes/Zoarcoidei | Lumpenidae | Neolumpenus unocellatus | native | Japanese : Montsuki-gaji | |
| Mugiliformes | Mugilidae | Neomyxus leuciscus | native | Acute-jawed mullet | Japanese : Kuchiboso-bora |
| Stomiiformes | Stomiidae | Neonesthes capensis | native | Cape snaggletooth | Japanese : Namidatokagegisu |
| Holocentriformes | Holocentridae | Neoniphon argenteus | native | Clearfin squirrelfish | Japanese : Hoso-ebisu |
| Holocentriformes | Holocentridae | Neoniphon aurolineatus | native | Yellowstriped squirrelfish | Japanese : Hohobeni-ittoudai |
| Holocentriformes | Holocentridae | Neoniphon opercularis | native | Blackfin squirrelfish | Japanese : Hireguro ittoudai |
| Holocentriformes | Holocentridae | Neoniphon sammara | native | Sammara squirrelfish | Japanese : Ukeguchi-ittoudai |
| Ovalentaria/misc | Pomacentridae | Neopomacentrus cyanomos | native | Regal demoiselle | Japanese : Kuro-ribon-suzumedai |
| Ovalentaria/misc | Pomacentridae | Neopomacentrus taeniurus | native | Freshwater demoiselle | Japanese : Ribon-suzumedai |
| Ovalentaria/misc | Pomacentridae | Neopomacentrus violascens | native | Violet demoiselle | Japanese : Sumire-suzumedai |
| Osmeriformes | Salangidae | Neosalangichthys ishikawae | native | Japanese : Ishikawa-shira-uo | |
| Osmeriformes | Salangidae | Neosalanx reganius | endemic | Japanese : Ariakehime-shira-uo | |
| Myctophiformes | Neoscopelidae | Neoscopelus macrolepidotus | native | Large-scaled lantern fish | Japanese : Soto-ori-iwashi |
| Myctophiformes | Neoscopelidae | Neoscopelus microchir | native | Shortfin neoscopelid | Japanese : Sango-iwashi |
| Myctophiformes | Neoscopelidae | Neoscopelus porosus | native | Spangleside neoscopelid | Japanese : Shichigo-iwashi |
| Perciformes/Scorpaenoidei | Neosebastidae | Neosebastes entaxis | native | Orange-banded scorpionfish | Japanese : Hirenagakasago |
| Perciformes/Zoarcoidei | Neozoarcidae | Neozoarces steindachneri | native | Japanese : Hanaitoginpo | |
| Scombriformes | Gempylidae | Nesiarchus nasutus | native | Black gemfish | Japanese : Hashinagakurotachi |
| Anguilliformes | Nettastomatidae | Nettastoma parviceps | native | Duck-billed eel | Japanese : Kuzu-anago |
| Anguilliformes | Nettastomatidae | Nettastoma solitarium | native | Solitary duckbill eel | Japanese : Nise-kuzu-anago |
| Siluriformes | Ariidae | Netuma bilineata | native | Bronze catfish | |
| Siluriformes | Ariidae | Netuma thalassina | native | Giant catfish | Japanese : Osaka-Hamagigi |
| Gadiformes | Macrouridae | Nezumia burragei | native | Japanese : Nanyôdara | |
| Gadiformes | Macrouridae | Nezumia condylura | native | Japanese pugnose grenadier | Japanese : Nezumidara |
| Gadiformes | Macrouridae | Nezumia kamoharai | native | Japanese : Sokodara | |
| Gadiformes | Macrouridae | Nezumia propinqua | native | Aloha grenadier | Japanese : Kiheri-nezumidara |
| Gadiformes | Macrouridae | Nezumia proxima | native | Short-tail grenadier | Japanese : Higo-sokodara |
| Gadiformes | Macrouridae | Nezumia rara | native | Japanese : Kakure-hige | |
| Gadiformes | Macrouridae | Nezumia shinoharai | native | Shinohara's grenadier | Japanese : Shinohara-hige |
| Gadiformes | Macrouridae | Nezumia spinosa | native | Sawspine whiptail | Japanese : Goten-hige |
| Gadiformes | Macrouridae | Nezumia tomiyamai | native | Japanese : Tomiyama-hige | |
| Eupercaria/misc | Sciaenidae | Nibea albiflora | native | Yellow drum | Japanese : Koichi |
| Eupercaria/misc | Sciaenidae | Nibea chui | native | Chu's croaker | |
| Eupercaria/misc | Sciaenidae | Nibea mitsukurii | native | Honnibe croaker | Japanese : Nibe |
| Eupercaria/misc | Sciaenidae | Nibea semifasciata | native | Sharpnose croaker | Japanese : Minami-nibe |
| Perciformes/Percoidei | Niphonidae | Niphon spinosus | native | Ara | Japanese : Ara |
| Cypriniformes | Xenocyprididae | Nipponocypris sieboldii | endemic | Japanese : Numamutsu | |
| Cypriniformes | Xenocyprididae | Nipponocypris temminckii | native | Dark chub | Japanese : Kawamutsu |
| Cypriniformes | Cobitidae | Niwaella delicata | native | Japanese : Ajime-dojô | |
| Scombriformes | Nomeidae | Nomeus gronovii | native | Man-of-war fish | Japanese : Eboshidai |
| Blenniiformes | Tripterygiidae | Norfolkia brachylepis | native | Tropical scaly-headed triplefin | |
| Blenniiformes | Tripterygiidae | Norfolkia thomasi | native | Thomas' triplefin | |
| Notacanthiformes | Notacanthidae | Notacanthus abbotti | native | Japanese : Kitsune-sokogisu | |
| Notacanthiformes | Notacanthidae | Notacanthus chemnitzii | native | Snubnosed spiny eel | Japanese : Kuro-sokogisu |
| Myctophiformes | Myctophidae | Notolychnus valdiviae | native | Topside lampfish | Japanese : Ura-hadaka |
| Rajiformes | Arhynchobatidae | Notoraja tobitukai | native | Leadhued skate | Japanese : Tobitsuka-ei |
| Hexanchiformes | Hexanchidae | Notorynchus cepedianus | native | Broadnose sevengill shark | Japanese : Ebisuzame |
| Myctophiformes | Myctophidae | Notoscopelus caudispinosus | native | Lobisomem | Japanese : Ôsebire-hadaka |
| Myctophiformes | Myctophidae | Notoscopelus japonicus | native | Japanese lanternfish | Japanese : Ôkuchi-iwashi |
| Myctophiformes | Myctophidae | Notoscopelus resplendens | native | Patchwork lampfish | Japanese : Isaribi-hadaka |
| Eupercaria/misc | Labridae | Novaculichthys taeniourus | native | Rockmover wrasse | Japanese : Obi-tensumodoki |
| Eupercaria/misc | Labridae | Novaculoides macrolepidotus | native | Seagrass wrasse | Japanese : Ôhire-tensumodoki |
| Eupercaria/misc | Labridae | Novaculops compressus | native | Garnet sandy | Japanese : Hokage-tensu-modoki |
| Eupercaria/misc | Labridae | Novaculops sciistius | native | Oriental sandy | |
| Acanthuriformes | Leiognathidae | Nuchequula nuchalis | native | Spotnape ponyfish | Japanese : Hiiragi |
| Gobiiformes | Gobiidae | Obliquogobius cirrifer | native | Japanese : Ito chihiro-haze | |
| Gobiiformes | Gobiidae | Obliquogobius fulvostriatus | native | ||
| Gobiiformes | Gobiidae | Obliquogobius megalops | native | Japanese : O'ome chihiro-haze | |
| Gobiiformes | Gobiidae | Obliquogobius trifasciatus | native | ||
| Gobiiformes | Gobiidae | Obliquogobius yamadai | native | ||
| Perciformes/Cottoidei | Agonidae | Occella dodecaedron | native | Bering poacher | Japanese : Kamutosachi-uo |
| Perciformes/Cottoidei | Agonidae | Occella iburia | native | Japanese : Saburô | |
| Perciformes/Cottoidei | Agonidae | Occella kasawae | native | Japanese : Yase-saburô | |
| Perciformes/Cottoidei | Agonidae | Occella kuronumai | native | Japanese : Shirô | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Ocosia fasciata | native | Japanese : Shima-hachi-okoze | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Ocosia vespa | native | Japanese : Hachi-okoze | |
| Perciformes/Cottoidei | Cottidae | Ocynectes maschalis | native | Japanese : Idaten-kajika | |
| Perciformes/Cottoidei | Cottidae | Ocynectes modestus | native | Japanese : Mutsu-kajika | |
| Gobiiformes | Gobiidae | Odontamblyopus lacepedii | native | Japanese : Warasubo | |
| Perciformes/Serranoidei | Anthiadidae | Odontanthias borbonius | native | Checked swallowtail | Japanese : Madara-hanadai |
| Perciformes/Serranoidei | Anthiadidae | Odontanthias flagris | native | Japanese : Hatatate-hanadai | |
| Perciformes/Serranoidei | Anthiadidae | Odontanthias katayamai | native | ||
| Perciformes/Serranoidei | Anthiadidae | Odontanthias rhodopeplus | native | Japanese : Boro-sakuradai | |
| Perciformes/Serranoidei | Anthiadidae | Odontanthias unimaculatus | native | Japanese : Itten-sakuradai | |
| Lamniformes | Odontaspididae | Odontaspis ferox | native | Smalltooth sand tiger | Japanese : Ôwanizame |
| Atheriniformes | Atherinopsidae | Odontesthes bonariensis | introduced | Argentinian silverside | Japanese : Rapurata-tougoroo |
| Gobiiformes | Odontobutidae | Odontobutis hikimius | native | Japanese : Ishi-donko | |
| Gobiiformes | Odontobutidae | Odontobutis obscurus | native | Japanese : Donko | |
| Aulopiformes | Evermannellidae | Odontostomops normalops | native | Undistinguished sabretooth | Japanese : Mukashi-yari-eso |
| Tetraodontiformes | Balistidae | Odonus niger | native | Red-toothed triggerfish | Japanese : Akamongara |
| Rajiformes | Rajidae | Okamejei acutispina | native | Sharpspine skate | Japanese : Moyôkasube |
| Rajiformes | Rajidae | Okamejei boesemani | native | Boeseman's skate | |
| Rajiformes | Rajidae | Okamejei hollandi | native | Yellow-spotted skate | Japanese : Isago-gangi-ei |
| Rajiformes | Rajidae | Okamejei kenojei | native | Ocellate spot skate | Japanese : Komonkasube |
| Rajiformes | Rajidae | Okamejei meerdervoortii | native | Bigeye skate | Japanese : Medamakasube |
| Rajiformes | Rajidae | Okamejei schmidti | native | Browneye skate | Japanese : Tsumarikasube |
| Gobiiformes | Gobiidae | Oligolepis acutipennis | native | Sharptail goby | Japanese : Noborihaze |
| Gobiiformes | Gobiidae | Oligolepis stomias | native | ||
| Blenniiformes | Blenniidae | Omobranchus elegans | native | Japanese : Nabeka | |
| Blenniiformes | Blenniidae | Omobranchus elongatus | native | Cloister blenny | Japanese : Goma-kumo-ginpo |
| Blenniiformes | Blenniidae | Omobranchus fasciolatoceps | native | Japanese : Tosakaginpo | |
| Blenniiformes | Blenniidae | Omobranchus ferox | native | Gossamer blenny | Japanese : Kawaginpo |
| Blenniiformes | Blenniidae | Omobranchus loxozonus | native | Japanese : Kumoginpo | |
| Blenniiformes | Blenniidae | Omobranchus punctatus | native | Muzzled blenny | |
| Aulopiformes | Omosudidae | Omosudis lowii | native | Omosudid | Japanese : Kiba-hadaka |
| Blenniiformes | Blenniidae | Omox biporos | native | Omox blenny | Japanese : Hirugiginpo |
| Salmoniformes | Salmonidae | Oncorhynchus gorbuscha | native | Pink salmon | Japanese : Karafutomasu |
| Salmoniformes | Salmonidae | Oncorhynchus iwame | endemic | Iwame trout | |
| Salmoniformes | Salmonidae | Oncorhynchus kawamurae | endemic | Kunimasu | Japanese : Kunimasu |
| Salmoniformes | Salmonidae | Oncorhynchus keta | native | Chum salmon | Japanese : Shiro-sake |
| Salmoniformes | Salmonidae | Oncorhynchus kisutch | native | Coho salmon | Japanese : Gin-zake |
| Salmoniformes | Salmonidae | Oncorhynchus masou | native | Masu salmon | Japanese : Amago; Japanese : Honmasu; |
| Salmoniformes | Salmonidae | Oncorhynchus mykiss | introduced | Rainbow trout | Japanese : Masu |
| Salmoniformes | Salmonidae | Oncorhynchus nerka | native | Sockeye salmon | Japanese : Himemasu |
| Salmoniformes | Salmonidae | Oncorhynchus rhodurus | native | Japanese Amago | Japanese : Biwamasu |
| Salmoniformes | Salmonidae | Oncorhynchus tshawytscha | native | Chinook salmon | Japanese : Masunosuke |
| Lophiiformes | Oneirodidae | Oneirodes bulbosus | native | Bulb-fish | Japanese : Yume-ankô |
| Lophiiformes | Oneirodidae | Oneirodes cordifer | native | ||
| Lophiiformes | Oneirodidae | Oneirodes eschrichtii | native | Bulbous dreamer | Japanese : Hime-rakuda-ankô |
| Lophiiformes | Oneirodidae | Oneirodes pietschi | native | ||
| Lophiiformes | Oneirodidae | Oneirodes thompsoni | native | Alaska dreamer | Japanese : Toge-rakuda-ankô |
| Perciformes/Scorpaenoidei | Platycephalidae | Onigocia bimaculata | native | Two-spotted flathead | Japanese : Sehoshi-omigochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Onigocia macrolepis | native | Notched flathead | Japanese : Anesagochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Onigocia spinosa | native | Midget flathead | Japanese : Onigochi |
| Ophidiiformes | Carapidae | Onuxodon parvibrachium | native | Oyster pearlfish | |
| Syngnathiformes | Syngnathidae | Oostethus jagorii | native | Japanese : Hime-tengu-yōji | |
| Anguilliformes | Ophichthidae | Ophichthus altipennis | native | Highfin snake eel | Japanese : Tongari-hotate-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus asakusae | native | Japanese : Inaka-umihebi | |
| Anguilliformes | Ophichthidae | Ophichthus cephalozona | native | Dark-shouldered snake eel | |
| Anguilliformes | Ophichthidae | Ophichthus erabo | native | Blotched snake-eel | Japanese : Mongaradôshi |
| Anguilliformes | Ophichthidae | Ophichthus kusanagi | native | Kusanagi snake eel | Japanese : Kusanagi-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus lithinus | native | Evermann's snake eel | Japanese : Hôrai-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus lupus | native | Lupine snake eel | Japanese : Yamainu-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus machidai | native | ||
| Anguilliformes | Ophichthidae | Ophichthus megalops | native | ||
| Anguilliformes | Ophichthidae | Ophichthus obtusus | native | ||
| Anguilliformes | Ophichthidae | Ophichthus oligosteus | native | Few-vertebrae snake eel | Japanese : Tsumari-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus pallens | native | Narrow-fin snake eel | Japanese : Tarumi-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus polyophthalmus | native | Many-eyed snake-eel | Japanese : Wanuke-mongaradôshi |
| Anguilliformes | Ophichthidae | Ophichthus roseus | native | ||
| Anguilliformes | Ophichthidae | Ophichthus tsuchidae | native | Japanese : Nishiki-umihebi | |
| Anguilliformes | Ophichthidae | Ophichthus urolophus | native | Manetail snake eel | Japanese : Suso-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus yamakawai | native | Ruler-pattern snake eel | Japanese : Monosashi-umihebi |
| Anguilliformes | Ophichthidae | Ophichthus zophistius | native | Temperate highfin snake eel | Japanese : Hotate-umihebi |
| Ophidiiformes | Ophidiidae | Ophidion asiro | native | Japanese : Ashiro | |
| Ophidiiformes | Ophidiidae | Ophidion muraenolepis | native | Blackedge cusk | Japanese : Ashiro |
| Gobiiformes | Butidae | Ophiocara gigas | native | Giant mud-gudgeon | Japanese : Kumo-madara-haze |
| Gobiiformes | Butidae | Ophiocara macrostoma | native | Dark-fin gudgeon | Japanese : Yami-madara-haze |
| Gobiiformes | Butidae | Ophiocara ophicephalus | native | Spangled gudgeon | Japanese : Hoshi-madara-haze |
| Anguilliformes | Ophichthidae | Ophisurus macrorhynchos | native | Japanese : Dainan-umihebi | |
| Anguilliformes | Ophichthidae | Ophisurus serpens | native | Serpent eel | |
| Perciformes/Zoarcoidei | Opisthocentridae | Opisthocentrus ocellatus | native | Ocellated blenny | Japanese : Gaji |
| Perciformes/Zoarcoidei | Opisthocentridae | Opisthocentrus tenuis | native | Japanese : Hanajiro-gaji | |
| Perciformes/Zoarcoidei | Opisthocentridae | Opisthocentrus zonope | native | Japanese : Okikazunagi | |
| Ovalentaria/misc | Opistognathidae | Opistognathus castelnaui | native | Castelnau's jawfish | Japanese : Wani-amadai |
| Ovalentaria/misc | Opistognathidae | Opistognathus evermanni | native | Rainbow jawfish | Japanese : Niji-amadai |
| Ovalentaria/misc | Opistognathidae | Opistognathus hopkinsi | native | Japanese : Ago-amadai | |
| Ovalentaria/misc | Opistognathidae | Opistognathus iyonis | native | Japanese : Nirami-amadai | |
| Ovalentaria/misc | Opistognathidae | Opistognathus liturus | native | Japanese : Seto-amadai | |
| Ovalentaria/misc | Opistognathidae | Opistognathus ocellicaudatus | native | Eyespottail jawfish | English : Eyespottail jawfish |
| Ovalentaria/misc | Opistognathidae | Opistognathus trimaculatus | native | Threespot jawfish | English : Threespot jawfish |
| Ovalentaria/misc | Opistognathidae | Opistognathus variabilis | native | Variable jawfish | |
| Centrarchiformes | Oplegnathidae | Oplegnathus fasciatus | native | Barred knifejaw | Japanese : Ishidai |
| Centrarchiformes | Oplegnathidae | Oplegnathus punctatus | native | Spotted knifejaw | Japanese : Ishigakidai |
| Gobiiformes | Gobiidae | Oplopomops diacanthus | native | Hole goby | |
| Gobiiformes | Gobiidae | Oplopomus oplopomus | native | Spinecheek goby | |
| Stomiiformes | Stomiidae | Opostomias mitsuii | native | Pitgum lanternfish | Japanese : Mitsui-hoshi-eso |
| Cypriniformes | Xenocyprididae | Opsariichthys uncirostris | native | Three-lips | Japanese : Hasu |
| Orectolobiformes | Orectolobidae | Orectolobus japonicus | native | Japanese wobbegong | Japanese : Ôse |
| Cichliformes | Cichlidae | Oreochromis aureus | introduced | Blue tilapia | |
| Cichliformes | Cichlidae | Oreochromis mossambicus | introduced | Mozambique tilapia | Japanese : Kawasuzume |
| Cichliformes | Cichlidae | Oreochromis niloticus | introduced | Nile tilapia | Japanese : Chikadai |
| Beloniformes | Adrianichthyidae | Oryzias latipes | native | Japanese rice fish | Japanese : Medaka |
| Beloniformes | Adrianichthyidae | Oryzias sakaizumii | native | Northern medaka | Japanese : Kitano-medaka |
| Beloniformes | Adrianichthyidae | Oryzias sinensis | native | ||
| Osmeriformes | Osmeridae | Osmerus dentex | native | Pacific rainbow smelt | Japanese : Kyûri-uo |
| Osmeriformes | Osmeridae | Osmerus mordax | native | Rainbow smelt | |
| Acropomatiformes | Hemerocoetidae | Osopsaron formosensis | native | ||
| Acropomatiformes | Hemerocoetidae | Osopsaron verecundum | native | Japanese : Himetoragisu | |
| Anabantiformes | Osphronemidae | Osphronemus goramy | introduced | Giant gourami | Japanese : Guurami |
| Mugiliformes | Mugilidae | Osteomugil cunnesius | native | Longarm mullet | Japanese : Nan-yô-bora |
| Mugiliformes | Mugilidae | Osteomugil engeli | native | Kanda | Japanese : Monnashi-bora |
| Mugiliformes | Mugilidae | Osteomugil perusii | native | Longfinned mullet | |
| Holocentriformes | Holocentridae | Ostichthys archiepiscopus | native | Straighthead soldierfish | Japanese : Oki-ebisu |
| Holocentriformes | Holocentridae | Ostichthys hypsipterygion | native | Highfin soldierfish | Japanese : Hiredaka-ebisu |
| Holocentriformes | Holocentridae | Ostichthys japonicus | native | Japanese soldierfish | Japanese : Ebisudai |
| Holocentriformes | Holocentridae | Ostichthys kaianus | native | Deepwater soldierfish | Japanese : Kai-ebisu |
| Kurtiformes | Apogonidae | Ostorhinchus angustatus | native | Broadstriped cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus apogonoides | native | Short-tooth cardinal | Japanese : Aohana-tenjikudai |
| Kurtiformes | Apogonidae | Ostorhinchus aureus | native | Ring-tailed cardinalfish | Japanese : Aosuji-tenjikudai |
| Kurtiformes | Apogonidae | Ostorhinchus cheni | native | Munahosi cardinalfish | Japanese : Munahosi-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus chrysotaenia | native | Yellowlined cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus compressus | native | Ochre-striped cardinalfish | Japanese : Hira-tenjikudai |
| Kurtiformes | Apogonidae | Ostorhinchus cookii | native | Cook's cardinalfish | Japanese : Suji-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus cyanosoma | native | Yellowstriped cardinalfish | Japanese : Kinsen-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus dispar | native | Redspot cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus doederleini | native | Doederlein's cardinalfish | Japanese : ôsuji-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus endekataenia | native | Candystripe cardinalfish | Japanese : Kosuji-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus fasciatus | native | Broadbanded cardinalfish | Japanese : Fûrai-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus fukuii | native | Japanese : Futasuji-ishimochi | |
| Kurtiformes | Apogonidae | Ostorhinchus hoevenii | native | Frostfin cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus ishigakiensis | native | Japanese : Miyako-ishimochi | |
| Kurtiformes | Apogonidae | Ostorhinchus jenkinsi | native | Spot-nape cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus kiensis | native | Rifle cardinal | Japanese : Teppô-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus moluccensis | native | Moluccan cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus nigrofasciatus | native | Blackstripe cardinalfish | Japanese : Minami-futosuji-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus notatus | native | Spotnape cardinalfish | Japanese : Kurohoshi-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus novemfasciatus | native | Sevenstriped cardinalfish | Japanese : Tasuji-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus parvulus | native | Japanese : Neon-tenjikudai | |
| Kurtiformes | Apogonidae | Ostorhinchus properuptus | native | Southern orange-lined cardinal fish | Japanese : Kinsen-ishimochi |
| Kurtiformes | Apogonidae | Ostorhinchus sealei | native | Seale's cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus selas | native | Meteor cardinalfish | |
| Kurtiformes | Apogonidae | Ostorhinchus semilineatus | native | Half-lined cardinal | Japanese : Nenbutsudai |
| Kurtiformes | Apogonidae | Ostorhinchus taeniophorus | native | Reef-flat cardinalfish | |
| Tetraodontiformes | Ostraciidae | Ostracion cubicum | native | Yellow boxfish | Japanese : Minami-hakofugu |
| Tetraodontiformes | Ostraciidae | Ostracion immaculatum | native | Bluespotted boxfish | Japanese : Hakofugu |
| Tetraodontiformes | Ostraciidae | Ostracion meleagris | native | Spotted boxfish | Japanese : Kuro-hakofugu |
| Tetraodontiformes | Ostraciidae | Ostracion rhinorhynchos | native | Horn-nosed boxfish | Japanese : Tengu-hakofugu |
| Acropomatiformes | Ostracoberycidae | Ostracoberyx dorygenys | native | Japanese : Tsunogashira | |
| Acropomatiformes | Ostracoberycidae | Ostracoberyx fowleri | native | Japanese : Onigashira | |
| Cichliformes | Cichlidae | Otopharynx lithobates | introduced | ||
| Eupercaria/misc | Cepolidae | Owstonia japonica | native | Japanese : Soko-amadai-modoki | |
| Eupercaria/misc | Cepolidae | Owstonia kamoharai | native | Kamohara's Bandfish | Japanese : Oh-soko-amadai |
| Eupercaria/misc | Cepolidae | Owstonia taeniosoma | native | Japanese : Akatachi-modoki | |
| Eupercaria/misc | Cepolidae | Owstonia tosaensis | native | Japanese : Oki-amadai | |
| Eupercaria/misc | Cepolidae | Owstonia totomiensis | native | Short-tail bandfish | Japanese : Soko-amadai |
| Gobiiformes | Oxudercidae | Oxuderces dentatus | native | ||
| Eupercaria/misc | Labridae | Oxycheilinus bimaculatus | native | Two-spot wrasse | Japanese : Takobera |
| Eupercaria/misc | Labridae | Oxycheilinus celebicus | native | Celebes wrasse | Japanese : Hananaga-mochino-uo; Japanese : Mochino-uo; |
| Eupercaria/misc | Labridae | Oxycheilinus digramma | native | Cheeklined wrasse | Japanese : Hôsuji-mochino-uo |
| Eupercaria/misc | Labridae | Oxycheilinus orientalis | native | Oriental maori wrasse | |
| Eupercaria/misc | Labridae | Oxycheilinus samurai | native | Black-tip Maori-wrasse | Japanese : Sakayaki-hohosuji-mochinouo |
| Eupercaria/misc | Labridae | Oxycheilinus unifasciatus | native | Ringtail maori wrasse | Japanese : Hitosuji-mochino-uo |
| Centrarchiformes | Cirrhitidae | Oxycirrhites typus | native | Longnose hawkfish | Japanese : Kudagonbe |
| Anguilliformes | Muraenesocidae | Oxyconger leptognathus | native | Shorttail pike conger | Japanese : Hashinaga-anago |
| Gobiiformes | Microdesmidae | Oxymetopon compressus | native | Robust ribbongoby | |
| Tetraodontiformes | Monacanthidae | Oxymonacanthus longirostris | native | Harlequin filefish | Japanese : Tengukawahagi |
| Squaliformes | Oxynotidae | Oxynotus japonicus | native | Japanese roughshark | Japanese : Oroshi zame |
| Beloniformes | Hemiramphidae | Oxyporhamphus micropterus | native | Bigwing halfbeak | Japanese : Sayori-tobi-uo |
| Gobiiformes | Gobiidae | Oxyurichthys auchenolepis | native | Scaly-nape tentacle goby | Japanese : Saruhaze |
| Gobiiformes | Gobiidae | Oxyurichthys cornutus | native | Horned tentacle goby | |
| Gobiiformes | Gobiidae | Oxyurichthys microlepis | native | Maned goby | |
| Gobiiformes | Gobiidae | Oxyurichthys mindanensis | native | ||
| Gobiiformes | Gobiidae | Oxyurichthys ophthalmonema | native | Eyebrow goby | Japanese : Matsugehaze |
| Gobiiformes | Gobiidae | Oxyurichthys papuensis | native | Frogface goby | |
| Gobiiformes | Gobiidae | Oxyurichthys visayanus | native | Japanese : Minami-saruhaze | |
| Gobiiformes | Gobiidae | Oxyurichthys zeta | native | ||
| Stomiiformes | Stomiidae | Pachystomias microdon | native | Smalltooth dragonfish | Japanese : Kurenai-hoshi-eso |
| Gobiiformes | Gobiidae | Paedogobius kimurai | native | Babyface goby | Japanese : Shirasu-kibahaze |
| Eupercaria/misc | Sparidae | Pagrus auratus | native | Silver seabream | |
| Eupercaria/misc | Sparidae | Pagrus major | native | Red seabream | Japanese : Tai |
| Perciformes/Cottoidei | Agonidae | Pallasina barbata | native | Tubenose poacher | Japanese : Higenaga-yagi-uo |
| Gobiiformes | Butidae | Paloa villadolidi | native | Japanese : Shīsā-haze | |
| Gobiiformes | Gobiidae | Palutrus meteori | native | Meteor goby | Japanese : Hime-kumohaze |
| Scombriformes | Stromateidae | Pampus argenteus | native | Silver pomfret | Japanese : Kôrai-managatsuo; Japanese : Managatsuo; |
| Scombriformes | Stromateidae | Pampus chinensis | native | Chinese silver pomfret | Japanese : Shina-managatsuo |
| Scombriformes | Stromateidae | Pampus cinereus | native | Grey pomfret | Japanese : Hirenaga-managatsuo |
| Scombriformes | Stromateidae | Pampus punctatissimus | native | Japanese : Managatsuo | |
| Gobiiformes | Gobiidae | Pandaka lidwilli | native | Lidwill's dwarfgoby | Japanese : Gomahaze |
| Gobiiformes | Gobiidae | Pandaka trimaculata | native | Japanese : Mitsuboshi-gomahaze | |
| Anguilliformes | Congridae | Parabathymyrus macrophthalmus | native | Japanese : Medama-anago | |
| Perciformes/Scorpaenoidei | Bembridae | Parabembras curta | native | Japanese : Ubagochi | |
| Blenniiformes | Blenniidae | Parablennius yatabei | native | Japanese : Isoginpo | |
| Pleuronectiformes | Bothidae | Parabothus coarctatus | native | Japanese : Sumiregarei | |
| Pleuronectiformes | Bothidae | Parabothus kiensis | native | Japanese : Kishûdarumagarei | |
| Cypriniformes | Botiidae | Parabotia curtus | endemic | Kissing loach | Japanese : Ayu-mokodi |
| Ophidiiformes | Bythitidae | Parabrotula plagiophthalma | native | False cusk | Japanese : Nise-itachiuo |
| Ophidiiformes | Bythitidae | Parabrotula tanseimaru | native | ||
| Eupercaria/misc | Lutjanidae | Paracaesio caerulea | native | Japanese snapper | Japanese : Aodai |
| Eupercaria/misc | Lutjanidae | Paracaesio kusakarii | native | Saddleback snapper | Japanese : Shima-aodai |
| Eupercaria/misc | Lutjanidae | Paracaesio sordida | native | Sordid snapper | Japanese : Yogore-aodai |
| Eupercaria/misc | Lutjanidae | Paracaesio stonei | native | Cocoa snapper | Japanese : Yanbaru-shima-aodai |
| Eupercaria/misc | Lutjanidae | Paracaesio xanthurus | native | Yellowtail blue snapper | Japanese : Umeiro |
| Acanthuriformes | Acanthuridae | Paracanthurus hepatus | native | Palette surgeonfish | Japanese : Nanyôhagi |
| Scombriformes | Caristiidae | Paracaristius nudarcus | native | ||
| Perciformes/Scorpaenoidei | Tetrarogidae | Paracentropogon rubripinnis | native | Japanese : Ha-okoze | |
| Acanthuriformes | Pomacanthidae | Paracentropyge multifasciata | native | Barred angelfish | Japanese : Shimayakko |
| Acanthuriformes | Chaetodontidae | Parachaetodon ocellatus | native | Sixspine butterflyfish | Japanese : Tentsuki-chôchô-uo |
| Gobiiformes | Gobiidae | Parachaeturichthys polynema | native | Taileyed goby | Japanese : Higehaze |
| Eupercaria/misc | Labridae | Paracheilinus carpenteri | native | Pink flasher | |
| Eupercaria/misc | Labridae | Paracheilinus lineopunctatus | native | Spot-lined flasher | |
| Centrarchiformes | Cirrhitidae | Paracirrhites arcatus | native | Arc-eye hawkfish | Japanese : Meganegonbe |
| Centrarchiformes | Cirrhitidae | Paracirrhites forsteri | native | Blackside hawkfish | Japanese : Hoshigonbe |
| Centrarchiformes | Cirrhitidae | Paracirrhites hemistictus | native | Whitespot hawkfish | Japanese : Irezumigonbe |
| Carcharhiniformes | Hemigaleidae | Paragaleus tengi | native | Straight-tooth weasel shark | Japanese : Ten-ibara zame |
| Gobiiformes | Gobiidae | Paragobiodon echinocephalus | native | Redhead goby | Japanese : Darumahaze |
| Gobiiformes | Gobiidae | Paragobiodon kasaii | native | Japanese : Kasai-darumahaze | |
| Gobiiformes | Gobiidae | Paragobiodon lacunicolus | native | Blackfin coral goby | Japanese : Panda-darumahaze |
| Gobiiformes | Gobiidae | Paragobiodon melanosoma | native | Dark coral goby | Japanese : Kuro-darumahaze |
| Gobiiformes | Gobiidae | Paragobiodon modestus | native | Warthead goby | Japanese : Yogore-darumahaze |
| Gobiiformes | Gobiidae | Paragobiodon xanthosoma | native | Emerald coral goby | Japanese : Akane-darumahaze |
| Perciformes/Scorpaenoidei | Peristediidae | Paraheminodus kamoharai | native | Kamohara's armored searobin | |
| Perciformes/Scorpaenoidei | Peristediidae | Paraheminodus laticephalus | native | Japanese : Kôtôkihôbô | |
| Perciformes/Scorpaenoidei | Peristediidae | Paraheminodus murrayi | native | Murray's armoured gurnard | Japanese : Hanabirokihôbô |
| Salmoniformes | Salmonidae | Parahucho perryi | native | Japanese huchen | Japanese : Itô |
| Eupercaria/misc | Labridae | Parajulis poecilepterus | native | Japanese : Kyûsen | |
| Pleuronectiformes | Paralichthyidae | Paralichthys olivaceus | native | Bastard halibut | Japanese : Hirame |
| Perciformes/Cottoidei | Liparidae | Paraliparis atramentatus | native | Japanese : Inki-uo | |
| Perciformes/Cottoidei | Liparidae | Paraliparis dipterus | native | Japanese : Suruga-inkiuo | |
| Perciformes/Cottoidei | Liparidae | Paraliparis mandibularis | native | Japanese : Ago-inki-uo | |
| Perciformes/Cottoidei | Liparidae | Paraliparis meridionalis | native | Japanese : Ryukyu-inki-uo | |
| Perciformes/Cottoidei | Liparidae | Paraliparis pectoralis | native | Japanese : Mune-inkiuo | |
| Perciformes/Cottoidei | Liparidae | Paraliparis rosaceus | native | Pink snailfish | Japanese : Ao-inki-uo |
| Perciformes/Cottoidei | Liparidae | Paraliparis ruficometes | native | Long-tailed snailfsh | Japanese : Onaga-inkiuo |
| Perciformes/Cottoidei | Liparidae | Paraliparis variabilidens | native | Variable-toothed snailfish | Japanese : Mitsuba-inkiuo |
| Tetraodontiformes | Monacanthidae | Paraluteres prionurus | native | False puffer | Japanese : Nokogirihagi |
| Ovalentaria/misc | Ambassidae | Parambassis ranga | introduced | Indian glassy fish | |
| Tetraodontiformes | Monacanthidae | Paramonacanthus japonicus | native | Hairfinned leatherjacket | Japanese : Yosogi |
| Tetraodontiformes | Monacanthidae | Paramonacanthus matsuurai | native | ||
| Tetraodontiformes | Monacanthidae | Paramonacanthus nipponensis | native | Japanese leatherjacket | Japanese : Tsuranagahagi |
| Tetraodontiformes | Monacanthidae | Paramonacanthus oblongus | native | Hair-finned filefish | |
| Tetraodontiformes | Monacanthidae | Paramonacanthus pusillus | native | Faintstripe filefish | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis aurantiaca | native | Japanese : Aka-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis basimaculata | native | Japanese : Sehoshi-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis clathrata | native | Latticed sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis cylindrica | native | Cylindrical sandperch | Japanese : Dandara-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis decemfasciata | native | Japanese : Yûdachi-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis kamoharai | native | Japanese : Kamohara-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis katoi | native | Japanese : Ogasawara-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis kentingensis | native | Kenting sandperch | English : Kenting sandperch |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis lutevittata | native | Yellow-striped sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis macrophthalma | native | Narrow barred grubfish | Japanese : Muro-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis millepunctata | native | Black dotted sand perch | Japanese : Wanuke-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis multifasciata | native | Gold-birdled sandsmelt | Japanese : Oki-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis multiplicata | native | Redbarred sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis muronis | native | Five-barred sandperch | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis natator | native | Japanese : Oyogi-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis okamurai | native | Japanese : Soko-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis ommatura | native | Japanese : Matô-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis pacifica | native | Japanese : Oguro toragisu; Japanese : Oguro-toragisu; | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis phenax | native | Japanese : Akaeri-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis pulchella | native | Harlequin sandsmelt | Japanese : Toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis schauinslandii | native | Redspotted sandperch | Japanese : Hawai-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis sexfasciata | native | Grub fish | Japanese : Kurakake-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis snyderi | native | U-mark sandperch | Japanese : Kôrai-toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis striolata | native | Japanese : Suji-toragisu | |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis tetracantha | native | Reticulated sandperch | Japanese : Madara toragisu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Parapercis xanthozona | native | Yellowbar sandperch | Japanese : Kokuten-toragisu |
| Pleuronectiformes | Cynoglossidae | Paraplagusia bilineata | native | Doublelined tonguesole | Japanese : Shirogarei |
| Pleuronectiformes | Cynoglossidae | Paraplagusia blochii | native | Bloch's tonguesole | Japanese : Nanyô-ushinoshita |
| Pleuronectiformes | Cynoglossidae | Paraplagusia japonica | native | Black cow-tongue | Japanese : Shitabirame |
| Perciformes/Scorpaenoidei | Aploactinidae | Paraploactis kagoshimensis | native | Japanese : Kagoshima-okoze | |
| Acropomatiformes | Pempheridae | Parapriacanthus ransonneti | native | Golden sweeper | Japanese : Kinmemodoki |
| Eupercaria/misc | Haemulidae | Parapristipoma trilineatum | native | Chicken grunt | Japanese : Isaki |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parapterois heterura | native | Blackfoot firefish | Japanese : Seto-minokasago |
| Eupercaria/misc | Nemipteridae | Parascolopsis akatamae | native | Rosy dwarf monocle bream | Japanese : Aka-tamagashira |
| Eupercaria/misc | Nemipteridae | Parascolopsis eriomma | native | Swallowtail dwarf monocle bream | Japanese : Shikoku-tamagashira |
| Eupercaria/misc | Nemipteridae | Parascolopsis inermis | native | Unarmed dwarf monocle bream | Japanese : Tamagashira |
| Eupercaria/misc | Nemipteridae | Parascolopsis tosensis | native | Tosa dwarf monocle bream | Japanese : Kisuji-tamagashira |
| Acropomatiformes | Synagropidae | Parascombrops analis | native | Threespine seabass | Japanese : Bake-sumikui-uo |
| Acropomatiformes | Synagropidae | Parascombrops mochizukii | native | ||
| Acropomatiformes | Synagropidae | Parascombrops nakayamai | native | ||
| Acropomatiformes | Synagropidae | Parascombrops ohei | endemic | ||
| Acropomatiformes | Synagropidae | Parascombrops philippinensis | native | Sharptooth seabass | Japanese : Hime-sumikui-uo |
| Acropomatiformes | Synagropidae | Parascombrops serratospinosus | native | Roughspine seabass | Japanese : Tsumari-hime-sumikui-uo |
| Acropomatiformes | Synagropidae | Parascombrops yamanouei | native | Yamanoue's seabass | Japanese : Sedaka-himesumikuiuo |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena aurita | native | Golden scorpionfish | Japanese : Madara-fusakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena maculipinnis | native | Japanese : Toge-itten-fusakasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena mcadamsi | native | McAdam's scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Parascorpaena mossambica | native | Mozambique scorpionfish | |
| Carangiformes | Carangidae | Parastromateus niger | native | Black pomfret | Japanese : Kuroaji-modoki |
| Tetraodontiformes | Triacanthodidae | Paratriacanthodes retrospinis | native | Sawspine spikefish | Japanese : Musujikawamuki |
| Gobiiformes | Gobiidae | Paratrypauchen microcephalus | native | Comb goby | Japanese : Aka-uo |
| Aulopiformes | Paraulopidae | Paraulopus brevirostris | native | Shortsnout cucumberfish | Japanese : Montsuki-aome-eso |
| Aulopiformes | Paraulopidae | Paraulopus filamentosus | native | Japanese : Itohiki-aome-eso | |
| Aulopiformes | Paraulopidae | Paraulopus japonicus | native | Japanese : Mon-aome-eso | |
| Aulopiformes | Paraulopidae | Paraulopus oblongus | native | Japanese : Naga-aome-eso | |
| Zeiformes | Parazenidae | Parazen pacificus | native | Parazen | Japanese : Beni-matôdai |
| Pleuronectiformes | Soleidae | Pardachirus pavoninus | native | Peacock sole | Japanese : Minami-ushinoshita |
| Blenniiformes | Blenniidae | Parenchelyurus hepburni | native | Hepburn's blenny | Japanese : Karasuginpo |
| Beloniformes | Exocoetidae | Parexocoetus brachypterus | native | Sailfin flyingfish | Japanese : Tsumari-tobiuo |
| Beloniformes | Exocoetidae | Parexocoetus mento | native | African sailfin flyingfish | Japanese : Bashô-tobi-uo |
| Gobiiformes | Microdesmidae | Parioglossus caeruleolineatus | native | Japanese : Kujaku-haze | |
| Gobiiformes | Microdesmidae | Parioglossus dotui | native | Japanese : Satsukihaze | |
| Gobiiformes | Microdesmidae | Parioglossus formosus | native | Beautiful hover goby | Japanese : Yosujihaze |
| Gobiiformes | Microdesmidae | Parioglossus interruptus | native | Interrupted dartfish | Japanese : Hime-satsukihaze |
| Gobiiformes | Microdesmidae | Parioglossus lineatus | native | Lined hover goby | Japanese : Maiko-haze |
| Gobiiformes | Microdesmidae | Parioglossus palustris | native | Borneo hoverer | Japanese : Boruneohaze |
| Gobiiformes | Microdesmidae | Parioglossus philippinus | native | Philippine dartfish | |
| Gobiiformes | Microdesmidae | Parioglossus rainfordi | native | Rainford's dartfish | Japanese : Kobito-haze |
| Gobiiformes | Microdesmidae | Parioglossus raoi | native | Rao's hover goby | Japanese : Miyarabihaze |
| Gobiiformes | Microdesmidae | Parioglossus senoui | native | Japanese : Musume-haze | |
| Gobiiformes | Microdesmidae | Parioglossus taeniatus | native | Taeniatus dartfish | Japanese : Komachi-haze |
| Gobiiformes | Gobiidae | Parkraemeria rhinoceros | native | Japanese : Tengu-ginpo-haze | |
| Gobiiformes | Gobiidae | Parkraemeria saltator | native | Japanese : Ginpohaze | |
| Carcharhiniformes | Pentanchidae | Parmaturus pilosus | native | Salamander shark | Japanese : Imorizame |
| Mulliformes | Mullidae | Parupeneus barberinoides | native | Bicolor goatfish | Japanese : Indo-himeji |
| Mulliformes | Mullidae | Parupeneus barberinus | native | Dotdash goatfish | Japanese : Ôsuji-himeji |
| Mulliformes | Mullidae | Parupeneus chrysopleuron | native | Yellowband goatfish | Japanese : Umihigoi |
| Mulliformes | Mullidae | Parupeneus ciliatus | native | Blacksaddle goatfish | Japanese : Hôrai-himeji |
| Mulliformes | Mullidae | Parupeneus crassilabris | native | Triplebar goatfish | Japanese : Ojisan |
| Mulliformes | Mullidae | Parupeneus cyclostomus | native | Goldsaddle goatfish | Japanese : Marukuchi-himeji |
| Mulliformes | Mullidae | Parupeneus heptacantha | native | Cinnabar goatfish | Japanese : Takasago-Himeji |
| Mulliformes | Mullidae | Parupeneus indicus | native | Indian goatfish | Japanese : Koban-himeji |
| Mulliformes | Mullidae | Parupeneus insularis | native | Twosaddle goatfish | |
| Mulliformes | Mullidae | Parupeneus multifasciatus | native | Manybar goatfish | |
| Mulliformes | Mullidae | Parupeneus pleurostigma | native | Sidespot goatfish | Japanese : Ryukyu-himeji |
| Mulliformes | Mullidae | Parupeneus spilurus | native | Blackspot goatfish | Japanese : Okina-himeji |
| Dactylopteriformes | Pegasidae | Pegasus laternarius | native | ||
| Dactylopteriformes | Pegasidae | Pegasus volitans | native | Longtail seamouth | Japanese : Tenguno-otoshigo |
| Centrarchiformes | Terapontidae | Pelates quadrilineatus | native | Fourlined terapon | Japanese : Yosuji-shimaisaki |
| Acropomatiformes | Pempheridae | Pempheris adusta | native | Dusky sweeper | |
| Acropomatiformes | Pempheridae | Pempheris familia | native | Ogasawara sweeper | Japanese : Bonin-hatampo |
| Acropomatiformes | Pempheridae | Pempheris japonica | native | Japanese : Tsumaguro-hatanpo | |
| Acropomatiformes | Pempheridae | Pempheris nyctereutes | native | Japanese : Mie-hatanpo | |
| Acropomatiformes | Pempheridae | Pempheris oualensis | native | Blackspot sweeper | Japanese : Ryukyu-hatanpo |
| Acropomatiformes | Pempheridae | Pempheris schwenkii | native | Silver sweeper | |
| Acropomatiformes | Pempheridae | Pempheris ufuagari | native | Crown sweeper | Japanese : Daito hatampo |
| Acropomatiformes | Pempheridae | Pempheris xanthoptera | native | Japanese : Minami-hatanpo | |
| Eupercaria/misc | Sciaenidae | Pennahia argentata | native | Silver croaker | Japanese : Shiro-guchi |
| Ophidiiformes | Ophidiidae | Penopus japonicus | native | ||
| Acropomatiformes | Pentacerotidae | Pentaceros japonicus | native | Japanese armorhead | Japanese : Tsubodai |
| Acropomatiformes | Pentacerotidae | Pentaceros wheeleri | native | Slender armorhead | Japanese : Kusakari-tsubodai |
| Eupercaria/misc | Nemipteridae | Pentapodus caninus | native | Small-toothed whiptail | Japanese : Kitsun-un |
| Eupercaria/misc | Nemipteridae | Pentapodus nagasakiensis | native | Japanese whiptail | Japanese : Ito-tamagashira |
| Eupercaria/misc | Nemipteridae | Pentapodus trivittatus | native | Three-striped whiptail | |
| Eupercaria/misc | Gerreidae | Pentaprion longimanus | native | Longfin mojarra | Japanese : Taiwansagi |
| Perciformes/Cottoidei | Agonidae | Percis japonica | native | Dragon poacher | Japanese : Inugochi |
| Perciformes/Cottoidei | Agonidae | Percis matsuii | native | Japanese : Tonbo-inugochi | |
| Gobiiformes | Oxudercidae | Periophthalmus argentilineatus | native | Barred mudskipper | Japanese : Minami-tobihaze |
| Gobiiformes | Oxudercidae | Periophthalmus modestus | native | Shuttles hoppfish | Japanese : Tobihaze |
| Perciformes/Scorpaenoidei | Peristediidae | Peristedion liorhynchus | native | Armoured gurnard | Japanese : Moyô-kihôbô |
| Perciformes/Scorpaenoidei | Peristediidae | Peristedion orientale | native | Japanese : Kihôbô | |
| Perciformes/Scorpaenoidei | Peristediidae | Peristedion riversandersoni | native | Japanese : Heri-kihôbô | |
| Tetraodontiformes | Monacanthidae | Pervagor aspricaudus | native | Orangetail filefish | |
| Tetraodontiformes | Monacanthidae | Pervagor janthinosoma | native | Blackbar filefish | |
| Tetraodontiformes | Monacanthidae | Pervagor melanocephalus | native | Redtail filefish | Japanese : Nishikikawahagi |
| Tetraodontiformes | Monacanthidae | Pervagor nigrolineatus | native | Blacklined filefish | |
| Blenniiformes | Blenniidae | Petroscirtes breviceps | native | Striped poison-fang blenny mimic | Japanese : Nijiginpo |
| Blenniiformes | Blenniidae | Petroscirtes mitratus | native | Floral blenny | Japanese : Hatatateginpo |
| Blenniiformes | Blenniidae | Petroscirtes springeri | native | Japanese : Futahoshi-nijiginpo | |
| Blenniiformes | Blenniidae | Petroscirtes variabilis | native | Variable sabretooth blenny | Japanese : Inuginpo |
| Perciformes/Cottoidei | Cottidae | Phasmatocottus ctenopterygius | native | Japanese : Kushibirekajika | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Phenacoscorpius trispinis | native | Noslit scorpionfish | Japanese : Togire-kasago |
| Gobiesociformes | Gobiesocidae | Pherallodichthys meshimaensis | native | Japanese : Meshima-uba-uo | |
| Gobiesociformes | Gobiesocidae | Pherallodus indicus | native | Smalldisc clingfish | Japanese : Hoso-uba-uo |
| Perciformes/Zoarcoidei | Opisthocentridae | Pholidapus dybowskii | native | Japanese : Muroranginpo | |
| Perciformes/Zoarcoidei | Pholidae | Pholis crassispina | native | Japanese : Take-ginpo | |
| Perciformes/Zoarcoidei | Pholidae | Pholis fasciata | native | Banded gunnel | Japanese : Himoginpo |
| Perciformes/Zoarcoidei | Pholidae | Pholis laeta | native | Crescent gunnel | |
| Perciformes/Zoarcoidei | Pholidae | Pholis nea | native | Japanese : Aya-ginpo | |
| Perciformes/Zoarcoidei | Pholidae | Pholis nebulosa | native | Tidepool gunnel | Japanese : Ginpo |
| Perciformes/Zoarcoidei | Pholidae | Pholis picta | native | Japanese : Nishikiginpo | |
| Lophiiformes | Linophrynidae | Photocorynus spiniceps | native | ||
| Stomiiformes | Stomiidae | Photonectes albipennis | native | Whitepen dragonfish | Japanese : Hotei-eso |
| Stomiiformes | Stomiidae | Photonectes margarita | native | Japanese : Hireguro-hotei-eso | |
| Acanthuriformes | Leiognathidae | Photopectoralis bindus | native | Orangefin ponyfish | Japanese : Nettai-hiiragi |
| Stomiiformes | Stomiidae | Photostomias guernei | native | Japanese : Hôki-boshi-eso | |
| Stomiiformes | Stomiidae | Photostomias tantillux | native | ||
| Alepocephaliformes | Alepocephalidae | Photostylus pycnopterus | native | Starry smooth-head | |
| Gobiiformes | Gobiidae | Phoxacromion kaneharai | native | ||
| Cypriniformes | Leuciscidae | Phoxinus jouyi | native | Japanese : Takahaya | |
| Cypriniformes | Leuciscidae | Phoxinus steindachneri | native | Japanese : Aburahaya | |
| Syngnathiformes | Syngnathidae | Phoxocampus belcheri | native | Rock pipefish | |
| Syngnathiformes | Syngnathidae | Phoxocampus diacanthus | native | Spined pipefish | |
| Syngnathiformes | Syngnathidae | Phoxocampus tetrophthalmus | native | Trunk-barred pipefish | Japanese : Hakuten-bôyôji |
| Carangiformes | Echeneidae | Phtheirichthys lineatus | native | Slender suckerfish | Japanese : Sujikoban |
| Lophiiformes | Oneirodidae | Phyllorhinichthys micractis | native | ||
| Gadiformes | Moridae | Physiculus chigodarana | native | Japanese : Bara-chigodara | |
| Gadiformes | Moridae | Physiculus japonicus | native | Japanese codling | Japanese : Chigodara |
| Gadiformes | Moridae | Physiculus nigripinnis | native | Japanese : Hireguro-chigodara | |
| Gadiformes | Moridae | Physiculus rhodopinnis | native | Japanese : Aka-chigodara | |
| Gadiformes | Moridae | Physiculus yoshidae | native | Japanese : Oshare-chigodara | |
| Ovalentaria/misc | Pseudochromidae | Pictichromis porphyrea | native | Magenta dottyback | Japanese : Kurenai-nise-suzume |
| Eupercaria/misc | Lutjanidae | Pinjalo lewisi | native | Red pinjalo | Japanese : Sedakatakasago |
| Anguilliformes | Ophichthidae | Pisodonophis cancrivorus | native | Longfin snake-eel | Japanese : Minami-hotate-umihebi |
| Pleuronectiformes | Samaridae | Plagiopsetta glossa | native | Tongue flatfish | Japanese : Berogarei |
| Blenniiformes | Blenniidae | Plagiotremus laudandus | native | Bicolour fangblenny | Japanese : Inaseginpo |
| Blenniiformes | Blenniidae | Plagiotremus rhinorhynchos | native | Bluestriped fangblenny | Japanese : Minamiginpo |
| Blenniiformes | Blenniidae | Plagiotremus tapeinosoma | native | Piano fangblenny | Japanese : Ten-kurosujiginpo |
| Mugiliformes | Mugilidae | Planiliza affinis | native | Eastern keelback mullet | Japanese : Sesuji-bora |
| Mugiliformes | Mugilidae | Planiliza carinata | native | Keeled mullet | Japanese : Sesuji-bora |
| Mugiliformes | Mugilidae | Planiliza haematocheilus | native | So-iuy mullet | Japanese : Menada |
| Mugiliformes | Mugilidae | Planiliza macrolepis | native | Largescale mullet | Japanese : Ko-bora |
| Mugiliformes | Mugilidae | Planiliza melinoptera | native | Otomebora mullet | |
| Mugiliformes | Mugilidae | Planiliza subviridis | native | Greenback mullet | Japanese : Anpin-bora |
| Acanthuriformes | Ephippidae | Platax boersii | native | Golden spadefish | |
| Acanthuriformes | Ephippidae | Platax orbicularis | native | Orbicular batfish | Japanese : Tsubame-uo |
| Acanthuriformes | Ephippidae | Platax pinnatus | native | Dusky batfish | Japanese : Akakukuri |
| Acanthuriformes | Ephippidae | Platax teira | native | Longfin batfish | Japanese : Mikazuki-tsubame-uo |
| Pleuronectiformes | Pleuronectidae | Platichthys bicoloratus | native | Stone flounder | Japanese : Ishigarei |
| Pleuronectiformes | Pleuronectidae | Platichthys stellatus | native | Starry flounder | Japanese : Numagarei |
| Beloniformes | Belonidae | Platybelone platyura | native | Keeled needlefish | Japanese : Hime-datsu |
| Scombriformes | Caristiidae | Platyberyx rhyton | native | ||
| Carangiformes | Carangidae | Platycaranx chrysophrys | native | Longnose trevally | Japanese : Hishi-yoroi-aji |
| Carangiformes | Carangidae | Platycaranx malabaricus | native | Malabar trevally | Japanese : Taiwan-yoroi-aji |
| Carangiformes | Carangidae | Platycaranx talamparoides | native | Imposter trevally | Japanese : Ao-kagami-aji |
| Perciformes/Scorpaenoidei | Platycephalidae | Platycephalus indicus | native | Bartail flathead | Japanese : Kochi |
| Gobiiformes | Gobiidae | Platygobiopsis tansei | native | Japanese : Beta-haze | |
| Torpediniformes | Platyrhinidae | Platyrhina hyugaensis | native | Hyuga fanray | Japanese : Onino-uchiwa |
| Torpediniformes | Platyrhinidae | Platyrhina tangi | native | Yellow-spotted fanray | Japanese : Uchiwazame |
| Osmeriformes | Plecoglossidae | Plecoglossus altivelis | native | Ayu sweetfish | Japanese : Ayu |
| Eupercaria/misc | Haemulidae | Plectorhinchus albovittatus | native | Two-striped sweetlips | Japanese : Daidai-koshōdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus chaetodonoides | native | Harlequin sweetlips | Japanese : Chôchô-koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus chrysotaenia | native | Yellow-striped sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus cinctus | native | Crescent sweetlips | Japanese : Koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus diagrammus | native | Striped sweetlips | Japanese : Musuji-koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus flavomaculatus | native | Lemonfish | Japanese : Oshare-koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus gibbosus | native | Harry hotlips | Japanese : Kuro-koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus lessonii | native | Lesson's thicklip | |
| Eupercaria/misc | Haemulidae | Plectorhinchus lineatus | native | Yellowbanded sweetlips | Japanese : Aya-koshôdai; Japanese : Shima-koshôdai; |
| Eupercaria/misc | Haemulidae | Plectorhinchus obscurus | native | Giant sweetlips | |
| Eupercaria/misc | Haemulidae | Plectorhinchus picus | native | Dotted sweetlips | Japanese : Ajia-koshôdai |
| Eupercaria/misc | Haemulidae | Plectorhinchus vittatus | native | Oriental sweetlips | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias altipinnatus | native | Japanese : Chigohanadai | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias azumanus | native | Azuma perchlet | Japanese : Azumahanadai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias clavatus | native | Club perchlet | Japanese : Ichimonji-hanadai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias japonicus | native | Japanese perchlet | Japanese : Kasumi-sakuradai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias kamii | native | Kami's perchlet | Japanese : Izuhanadai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias kojiorum | native | ||
| Perciformes/Serranoidei | Anthiadidae | Plectranthias longimanus | native | Longfin perchlet | Japanese : Chibi-hanadai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias ryukyuensis | native | ||
| Perciformes/Serranoidei | Anthiadidae | Plectranthias sagamiensis | native | Japanese : Nishikihanadai | |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias takasei | native | Hinomaru perchlet | Japanese : Hinomaru-hanadai |
| Perciformes/Serranoidei | Anthiadidae | Plectranthias yamakawai | native | Japanese : Amami-hanadai | |
| Perciformes/Scorpaenoidei | Plectrogeniidae | Plectrogenium nanum | native | Japanese : Hime-kichiji | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon altus | native | Japanese gregory | Japanese : Sedaka-suzumedai |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon dickii | native | Blackbar devil | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon fasciolatus | native | Pacific gregory | Japanese : Fuchidori-suzumedai |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon imparipennis | native | Brighteye damselfish | Japanese : Iwasaki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon insularis | native | Island gregory | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon johnstonianus | native | Johnston Island damsel | Japanese : Rurime-ishigaki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon leucozonus | native | Singlebar devil | Japanese : Hakusen-suzumedai |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon obreptus | native | Western gregory | |
| Ovalentaria/misc | Pomacentridae | Plectroglyphidodon phoenixensis | native | Phoenix devil | Japanese : Fenikkusu-suzumedai |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus areolatus | native | Squaretail coralgrouper | Japanese : O-aonome-ara |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus laevis | native | Blacksaddled coralgrouper | Japanese : Kokuhan-ara |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus leopardus | native | Leopard coralgrouper | Japanese : Suji-ara |
| Perciformes/Serranoidei | Epinephelidae | Plectropomus maculatus | native | Spotted coralgrouper | Japanese : Suji-hata |
| Holocentriformes | Holocentridae | Plectrypops lima | native | Shy soldier | Japanese : Ryukyu-ebisu |
| Myliobatiformes | Plesiobatidae | Plesiobatis daviesi | native | Deep-water stingray | Japanese : Usu-ei |
| Ovalentaria/misc | Plesiopidae | Plesiops cephalotaenia | native | Headstripe longfin | Japanese : Yosaku-tanabata-uo |
| Ovalentaria/misc | Plesiopidae | Plesiops coeruleolineatus | native | Crimsontip longfin | Japanese : Tanabata-uo |
| Ovalentaria/misc | Plesiopidae | Plesiops corallicola | native | Bluegill longfin | Japanese : Donko-tanabata-uo |
| Ovalentaria/misc | Plesiopidae | Plesiops nakaharae | native | Japanese : Nakahara-tanabata-uo | |
| Ovalentaria/misc | Plesiopidae | Plesiops oxycephalus | native | Sharp-nosed longfin | Japanese : Okinawa-tanabata-uo |
| Ovalentaria/misc | Plesiopidae | Plesiops verecundus | native | Redtip longfin | |
| Perciformes/Cottoidei | Hexagrammidae | Pleurogrammus azonus | native | Okhotsk atka mackerel | Japanese : Hokke |
| Perciformes/Cottoidei | Hexagrammidae | Pleurogrammus monopterygius | native | Atka mackerel | Japanese : Kitano-hokke |
| Pleuronectiformes | Pleuronectidae | Pleuronectes quadrituberculatus | native | Alaska plaice | Japanese : Tsunogarei |
| Pleuronectiformes | Pleuronectidae | Pleuronichthys cornutus | native | Ridged-eye flounder | Japanese : Meita-garei; Japanese : Nagare-meitagarei; |
| Pleuronectiformes | Pleuronectidae | Pleuronichthys lighti | native | Common frog flounder | |
| Gobiiformes | Gobiidae | Pleurosicya bilobata | native | Bilobed ghost goby | Japanese : Umishôbuhaze |
| Gobiiformes | Gobiidae | Pleurosicya boldinghi | native | Soft-coral goby | |
| Gobiiformes | Gobiidae | Pleurosicya labiata | native | Barrel-sponge ghostgoby | |
| Gobiiformes | Gobiidae | Pleurosicya mossambica | native | Toothy goby | |
| Mugiliformes | Mugilidae | Plicomugil labiosus | native | Hornlip mullet | Japanese : Waniguchi-bora |
| Siluriformes | Plotosidae | Plotosus canius | native | Gray eel-catfish | |
| Siluriformes | Plotosidae | Plotosus japonicus | native | ||
| Siluriformes | Plotosidae | Plotosus lineatus | native | Striped eel catfish | Japanese : Gonzui |
| Perciformes/Cottoidei | Agonidae | Podothecus sachi | native | Snail-fin poacher | Japanese : Tokubire |
| Perciformes/Cottoidei | Agonidae | Podothecus sturioides | native | Japanese : Same-tokubire | |
| Cyprinodontiformes | Poeciliidae | Poecilia reticulata | introduced | Guppy | Japanese : Guppii |
| Cyprinodontiformes | Poeciliidae | Poecilia sphenops | introduced | Molly | |
| Pleuronectiformes | Poecilopsettidae | Poecilopsetta plinthus | native | Tile-colored righteye flounder | Japanese : Kawaragarei |
| Perciformes/Serranoidei | Grammistidae | Pogonoperca punctata | native | Bearded soapfish | Japanese : Agohata |
| Stomiiformes | Phosichthyidae | Pollichthys mauli | native | Stareye lightfish | Japanese : Yôji-eso |
| Notacanthiformes | Notacanthidae | Polyacanthonotus challengeri | native | Longnose tapirfish | Japanese : Sokogisu |
| Carangaria/misc | Polynemidae | Polydactylus plebeius | native | Striped threadfin | Japanese : Tsubame-konoshiro |
| Carangaria/misc | Polynemidae | Polydactylus sexfilis | native | Sixfinger threadfin | Japanese : Nanyô-agonashi |
| Carangaria/misc | Polynemidae | Polydactylus sextarius | native | Blackspot threadfin | Japanese : Kataguro-agonashi |
| Stomiiformes | Sternoptychidae | Polyipnus fraseri | native | Japanese : Tsuno-hônen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus matsubarai | native | Japanese : Hoshi-hônen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus parini | native | Japanese : Maru-hônen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus spinifer | native | Japanese : Nokoba-hônen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus stereope | native | Japanese : Kata-hônen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus surugaensis | native | Japanese : Suruga-hounen-eso | |
| Stomiiformes | Sternoptychidae | Polyipnus triphanos | native | Threelight hatchetfish | Japanese : Mitsuyubi-hônen-eso |
| Eupercaria/misc | Labridae | Polylepion russelli | native | Japanese : Kisuji-akabô | |
| Stomiiformes | Phosichthyidae | Polymetme corythaeola | native | Rendezvous fish | Japanese : Ginhadaka |
| Stomiiformes | Phosichthyidae | Polymetme elongata | native | Japanese : Ryûgûhadaka | |
| Stomiiformes | Phosichthyidae | Polymetme surugaensis | native | Suruga lightfish | Japanese : Tamabuki-iwashi |
| Polymixiiformes | Polymixiidae | Polymixia berndti | native | Pacific beardfish | Japanese : Arameginme |
| Polymixiiformes | Polymixiidae | Polymixia japonica | native | Silver eye | Japanese : Ginmedai |
| Polymixiiformes | Polymixiidae | Polymixia longispina | native | ||
| Perciformes/Cottoidei | Liparidae | Polypera simushirae | native | ||
| Acanthuriformes | Pomacanthidae | Pomacanthus annularis | native | Bluering angelfish | Japanese : Wanukeyakko |
| Acanthuriformes | Pomacanthidae | Pomacanthus imperator | native | Emperor angelfish | Japanese : Tatejima-kinchakudai |
| Acanthuriformes | Pomacanthidae | Pomacanthus semicirculatus | native | Semicircle angelfish | Japanese : Sazanami-yakko |
| Acanthuriformes | Pomacanthidae | Pomacanthus sexstriatus | native | Sixbar angelfish | Japanese : Rokusen-yakko |
| Acanthuriformes | Pomacanthidae | Pomacanthus xanthometopon | native | Yellowface angelfish | Japanese : Adeyakko |
| Ovalentaria/misc | Pomacentridae | Pomacentrus alexanderae | native | Alexander's damsel | Japanese : Montsuki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus amboinensis | native | Ambon damsel | Japanese : Nise-nettai-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus bankanensis | native | Speckled damselfish | Japanese : Megane-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus brachialis | native | Charcoal damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus chrysurus | native | Whitetail damsel | Japanese : Ojiro-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus coelestis | native | Neon damselfish | Japanese : Sora-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus lepidogenys | native | Scaly damsel | Japanese : Asado-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus moluccensis | native | Lemon damsel | Japanese : Nettai-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus nagasakiensis | native | Nagasaki damsel | Japanese : Nagasaki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus nigromarginatus | native | Blackmargined damsel | Japanese : Nise-montsuki-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus pavo | native | Sapphire damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus philippinus | native | Philippine damsel | Japanese : Firipin-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus simsiang | native | Blueback damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus smithi | native | Smith's damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus taeniometopon | native | Brackish damsel | Japanese : Sumizome-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomacentrus tripunctatus | native | Threespot damsel | |
| Ovalentaria/misc | Pomacentridae | Pomacentrus vaiuli | native | Princess damsel | Japanese : Kuro-megane-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pomachromis richardsoni | native | Richardson's reef-damsel | Japanese : Okinawa-suzumedai |
| Eupercaria/misc | Haemulidae | Pomadasys argenteus | native | Silver grunt | Japanese : Mizoisaki |
| Eupercaria/misc | Haemulidae | Pomadasys kaakan | native | Javelin grunter | |
| Eupercaria/misc | Haemulidae | Pomadasys maculatus | native | Saddle grunt | Japanese : Madara-mizoisaki |
| Eupercaria/misc | Haemulidae | Pomadasys quadrilineatus | native | Yellow-lined grunter | Japanese : Suji-mizoisaki |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pontinus macrocephalus | native | Largehead scorpionfish | Japanese : Hiodoshi |
| Perciformes/Cottoidei | Cottidae | Porocottus allisi | native | Japanese : Fusakajika | |
| Perciformes/Cottoidei | Cottidae | Porocottus coronatus | native | Japanese : Kanmuri-fusakajika | |
| Perciformes/Cottoidei | Cottidae | Porocottus japonicus | native | ||
| Perciformes/Cottoidei | Cottidae | Porocottus tentaculatus | native | Japanese : Itofusakajika | |
| Ophidiiformes | Ophidiidae | Porogadus dracocephalus | native | ||
| Ophidiiformes | Ophidiidae | Porogadus guentheri | native | Japanese : Tara-itachiuo | |
| Ophidiiformes | Ophidiidae | Porogadus trichiurus | native | ||
| Beryciformes | Melamphaidae | Poromitra cristiceps | native | ||
| Beryciformes | Melamphaidae | Poromitra curilensis | native | ||
| Beryciformes | Melamphaidae | Poromitra oscitans | native | Yawning | Japanese : Chihiro-kabuto-uo |
| Blenniiformes | Blenniidae | Praealticus labrovittatus | native | Crenulate-lipped rockskipper | |
| Blenniiformes | Blenniidae | Praealticus margaritarius | native | Japanese : Tamaginpo | |
| Blenniiformes | Blenniidae | Praealticus tanegasimae | native | Japanese : Taneginpo | |
| Eupercaria/misc | Priacanthidae | Priacanthus fitchi | native | Deepsea bigeye | |
| Eupercaria/misc | Priacanthidae | Priacanthus hamrur | native | Moontail bullseye | Japanese : Hôseki-kintoki |
| Eupercaria/misc | Priacanthidae | Priacanthus macracanthus | native | Red bigeye | Japanese : Kintokidai |
| Eupercaria/misc | Priacanthidae | Priacanthus sagittarius | native | Arrowfin bigeye | Japanese : Minami-kintoki |
| Eupercaria/misc | Priacanthidae | Priacanthus zaiserae | native | Miyake bigeye | Japanese : Kibire-kintoki |
| Gobiiformes | Gobiidae | Priolepis akihitoi | native | Emperor reefgoby | Japanese : Kokuten-benkeihaze |
| Gobiiformes | Gobiidae | Priolepis boreus | native | Japanese : Misaki-sujihaze | |
| Gobiiformes | Gobiidae | Priolepis cincta | native | Banded reef goby | Japanese : Benkeihaze |
| Gobiiformes | Gobiidae | Priolepis farcimen | native | Farcimen goby | |
| Gobiiformes | Gobiidae | Priolepis inhaca | native | Brick goby | Japanese : Amime-benkeihaze |
| Gobiiformes | Gobiidae | Priolepis latifascima | native | ||
| Gobiiformes | Gobiidae | Priolepis semidoliata | native | Half-barred goby | Japanese : Irezumihaze |
| Gobiiformes | Gobiidae | Priolepis winterbottomi | native | Japanese : Sakura-irezumi-haze | |
| Carcharhiniformes | Carcharhinidae | Prionace glauca | native | Blue shark | Japanese : Yoshikirizame |
| Acanthuriformes | Acanthuridae | Prionurus microlepidotus | native | Sixplate sawtail | |
| Acanthuriformes | Acanthuridae | Prionurus scalprum | native | Scalpel sawtail | Japanese : Nizadai |
| Kurtiformes | Apogonidae | Pristiapogon exostigma | native | Narrowstripe cardinalfish | Japanese : Yukata-ishimochi |
| Kurtiformes | Apogonidae | Pristiapogon fraenatus | native | Bridled cardinalfish | Japanese : Hitosuji-ishimochi |
| Kurtiformes | Apogonidae | Pristiapogon kallopterus | native | Iridescent cardinalfish | Japanese : Kasuri-ishimochi |
| Kurtiformes | Apogonidae | Pristicon rufus | native | Rufus cardinalfish | Japanese : Akahire-ishimochi |
| Kurtiformes | Apogonidae | Pristicon trimaculatus | native | Threespot cardinalfish | Japanese : Misuji-akahire-ishimochi |
| Eupercaria/misc | Priacanthidae | Pristigenys niphonia | native | Japanese bigeye | Japanese : Kurumadai |
| Eupercaria/misc | Priacanthidae | Pristigenys refulgens | native | Blackfringe Bigeye | Japanese : Minami-kurumadai |
| Holocentriformes | Holocentridae | Pristilepis oligolepis | native | Spinyface soldier | Japanese : Yase-ebisu |
| Pristiophoriformes | Pristiophoridae | Pristiophorus japonicus | native | Japanese sawshark | Japanese : Nokogirizame |
| Eupercaria/misc | Lutjanidae | Pristipomoides argyrogrammicus | native | Ornate jobfish | Japanese : Hanafuedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides auricilla | native | Goldflag jobfish | Japanese : Kimadara-himedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides filamentosus | native | Crimson jobfish | Japanese : Ôhime |
| Eupercaria/misc | Lutjanidae | Pristipomoides flavipinnis | native | Golden eye jobfish | Japanese : Kinme-himedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides multidens | native | Goldbanded jobfish | Japanese : Nagasakifuedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides sieboldii | native | Lavender jobfish | Japanese : Himedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides typus | native | Sharptooth jobfish | Japanese : Bara-himedai |
| Eupercaria/misc | Lutjanidae | Pristipomoides zonatus | native | Oblique-banded snapper | Japanese : Shimachibiki |
| Ovalentaria/misc | Pomacentridae | Pristotis obtusirostris | native | Gulf damselfish | Japanese : Oki-suzumedai |
| Scombriformes | Gempylidae | Promethichthys prometheus | native | Roudi escolar | Japanese : Kuroshibikamasu |
| Gobiesociformes | Gobiesocidae | Propherallodus briggsi | endemic | Japanese : Hime-uba-uo | |
| Carcharhiniformes | Proscylliidae | Proscyllium habereri | native | Graceful catshark | Japanese : Hyôzame |
| Carcharhiniformes | Proscylliidae | Proscyllium venustum | native | Japanese : Hyōzame | |
| Myctophiformes | Myctophidae | Protomyctophum crockeri | native | California flashlightfish | Japanese : Mukashi-hadaka |
| Myctophiformes | Myctophidae | Protomyctophum thompsoni | native | Bigeye lanternfish | Japanese : Ôme-hadaka |
| Eupercaria/misc | Sciaenidae | Protonibea diacanthus | native | Blackspotted croaker | Japanese : Goma-nibe |
| Gobiiformes | Gobiidae | Psammogobius biocellatus | native | Sleepy goby | Japanese : Hitomihaze |
| Carangaria/misc | Latidae | Psammoperca waigiensis | native | Waigieu seaperch | Japanese : Akame-modoki |
| Scombriformes | Nomeidae | Psenes arafurensis | native | Banded driftfish | Japanese : Kurage-uo |
| Scombriformes | Nomeidae | Psenes cyanophrys | native | Freckled driftfish | Japanese : Suji-hanabira-uo |
| Scombriformes | Nomeidae | Psenes maculatus | native | Silver driftfish | Japanese : Shima-hanabira-uo |
| Scombriformes | Nomeidae | Psenes pellucidus | native | Bluefin driftfish | Japanese : Hanabira-uo |
| Scombriformes | Centrolophidae | Psenopsis anomala | native | Pacific rudderfish | Japanese : Ibodai |
| Scombriformes | Centrolophidae | Psenopsis shojimai | native | Japanese : Nise-ibodai | |
| Pleuronectiformes | Bothidae | Psettina gigantea | native | Rough-scaled flounder | Japanese : Sokodarumagarei |
| Pleuronectiformes | Bothidae | Psettina iijimae | native | Japanese : Iijimadarumagarei | |
| Pleuronectiformes | Bothidae | Psettina tosana | native | Japanese : Tosadarumagarei | |
| Pleuronectiformes | Psettodidae | Psettodes erumei | native | Indian halibut | Japanese : Bozu Garei |
| Perciformes/Zoarcoidei | Stichaeidae | Pseudalectrias tarasovi | native | ||
| Tetraodontiformes | Monacanthidae | Pseudalutarius nasicornis | native | Rhinoceros leatherjacket | Japanese : Hanatsunohagi |
| Kurtiformes | Apogonidae | Pseudamia gelatinosa | native | Gelatinous cardinalfish | Japanese : Numeri-tenjikudai |
| Kurtiformes | Apogonidae | Pseudamia hayashii | native | Hayashi's cardinalfish | Japanese : Sabi-kudaribôzugisumodoki |
| Kurtiformes | Apogonidae | Pseudamia rubra | native | ||
| Kurtiformes | Apogonidae | Pseudamia zonata | native | Paddlefish cardinalfish | Japanese : Shima-kudaribôzugisumodoki |
| Kurtiformes | Apogonidae | Pseudamiops gracilicauda | native | Graceful-tailed cardinalfish | Japanese : Kudaribôzugisumodoki |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias caudalis | native | Japanese : Bara-nagahanadai | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias cichlops | native | Japanese : Kumasohanadai | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias cooperi | native | Red-bar anthias | Japanese : Kashiwahanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias elongatus | native | Japanese : Nagahanadai | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias fasciatus | native | One-stripe anthias | Japanese : Sujihanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias hypselosoma | native | Stocky anthias | Japanese : Keramahanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias leucozonus | endemic | Japanese : Shiro-obihanadai | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias luzonensis | native | Yellowlined anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias nobilis | native | ||
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias pleurotaenia | native | Square-spot fairy basslet | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias randalli | native | Randall's fairy basslet | Japanese : Fuchidorihanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias rubrizonatus | native | Red-belted anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias rubrolineatus | native | Thread-tail basslet | Japanese : Itohiki-kohaku-hanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias squamipinnis | native | Sea goldie | Japanese : Kingyohanadai |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias taira | native | Japanese : Ryukyuhanadai | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias tequila | native | Cave anthias | English : Cave anthias |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias thompsoni | native | Hawaiian anthias | |
| Perciformes/Serranoidei | Anthiadidae | Pseudanthias venator | native | Japanese : Kumaso-hanadai | |
| Gobiiformes | Oxudercidae | Pseudapocryptes elongatus | native | ||
| Cypriniformes | Leuciscidae | Pseudaspius brandtii | native | Pacific redfin | Japanese : Maruta ugui |
| Cypriniformes | Leuciscidae | Pseudaspius hakonensis | native | Big-scaled redfin | Japanese : Ugui |
| Cypriniformes | Leuciscidae | Pseudaspius nakamurai | native | Japanese : Ukekuchi-ugui | |
| Cypriniformes | Leuciscidae | Pseudaspius sachalinensis | native | Japanese : Ezo-ugui | |
| Anguilliformes | Muraenidae | Pseudechidna brummeri | native | White ribbon eel | Japanese : Moyou-take-utsubo |
| Siluriformes | Bagridae | Pseudobagrus tokiensis | native | Japanese : Gibachi | |
| Tetraodontiformes | Balistidae | Pseudobalistes flavimarginatus | native | Yellowmargin triggerfish | Japanese : Kiherimongara |
| Tetraodontiformes | Balistidae | Pseudobalistes fuscus | native | Yellow-spotted triggerfish | Japanese : Isomongara |
| Argentiniformes | Bathylagidae | Pseudobathylagus milleri | native | Stout blacksmelt | Japanese : Kuro-soko-iwashi |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius argenteus | native | Japanese : Yanagi-anahaze | |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius cottoides | native | Japanese : Asahi-anahaze | |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius marmoratus | native | Japanese : Aya-anahaze | |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius percoides | native | Sunrise | Japanese : Anahaze |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius totomius | native | Japanese : Hama-anahaze | |
| Perciformes/Cottoidei | Cottidae | Pseudoblennius zonostigma | native | Japanese : Obi-anahaze | |
| Callionymiformes | Callionymidae | Pseudocalliurichthys variegatus | native | Variegated ruddertail dragonet | Japanese : Itohiki-numeri |
| Carangiformes | Carangidae | Pseudocaranx dentex | native | White trevally | Japanese : Shimaaji |
| Lamniformes | Pseudocarchariidae | Pseudocarcharias kamoharai | native | Crocodile shark | Japanese : Mizuwani |
| Eupercaria/misc | Labridae | Pseudocheilinus evanidus | native | Striated wrasse | Japanese : Hime-nisemochino-uo |
| Eupercaria/misc | Labridae | Pseudocheilinus hexataenia | native | Sixline wrasse | Japanese : Nisemochino-uo |
| Eupercaria/misc | Labridae | Pseudocheilinus ocellatus | native | Whitebarred pink wrasse | |
| Eupercaria/misc | Labridae | Pseudocheilinus octotaenia | native | Eight-lined wrasse | Japanese : Yasuji-nisemochino-uo |
| Eupercaria/misc | Labridae | Pseudocheilinus tetrataenia | native | Four-lined wrasse | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis cyanotaenia | native | Surge dottyback | Japanese : Ryukyu-nisesuzume |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis fuscus | native | Brown dottyback | Japanese : Kibire-nisesuzume |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis luteus | native | ||
| Ovalentaria/misc | Pseudochromidae | Pseudochromis marshallensis | native | Marshall Is. dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis perspicillatus | native | Southeast Asian blackstripe dottyback | |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis tapeinosoma | native | Blackmargin dottyback | Japanese : Katsuiro-nisesuzume |
| Ovalentaria/misc | Pseudochromidae | Pseudochromis yamasakii | native | Dottybelly dottyback | Japanese : Haraten-nisesuzume |
| Eupercaria/misc | Labridae | Pseudocoris aurantiofasciata | native | Rust-banded wrasse | |
| Eupercaria/misc | Labridae | Pseudocoris bleekeri | native | Philippines wrasse | Japanese : Shiratakibera |
| Eupercaria/misc | Labridae | Pseudocoris heteroptera | native | Torpedo wrasse | Japanese : Shiratakibera-damashi |
| Eupercaria/misc | Labridae | Pseudocoris yamashiroi | native | Redspot wrasse | Japanese : Yamashirobera |
| Eupercaria/misc | Labridae | Pseudodax moluccanus | native | Chiseltooth wrasse | |
| Cypriniformes | Gobionidae | Pseudogobio esocinus | native | Japanese : Kamatsuka | |
| Gobiiformes | Gobiidae | Pseudogobius masago | native | Masago snubnose goby | Japanese : Masagohaze |
| Gobiiformes | Gobiidae | Pseudogobius melanosticta | native | Black-spotted snubnose goby | |
| Gobiiformes | Gobiidae | Pseudogobius poicilosoma | native | Northern fatnose goby | Japanese : Sunagohaze |
| Perciformes/Serranoidei | Grammistidae | Pseudogramma polyacantha | native | Honeycomb podge | Japanese : Togemegisu |
| Eupercaria/misc | Labridae | Pseudojuloides mesostigma | native | Sidespot wrasse | |
| Eupercaria/misc | Labridae | Pseudojuloides paradiseus | native | Paradise pencil wrasse | English : Paradise pencil wrasse |
| Eupercaria/misc | Labridae | Pseudojuloides pluto | native | Narcissus pencil wrasse | |
| Eupercaria/misc | Labridae | Pseudojuloides severnsi | native | Severns' wrasse | |
| Eupercaria/misc | Labridae | Pseudojuloides splendens | native | Splendid pencil wrasse | Japanese : Ogurobera |
| Eupercaria/misc | Labridae | Pseudolabrus eoethinus | native | Red naped wrasse | Japanese : Aka-sasanoha-bera |
| Eupercaria/misc | Labridae | Pseudolabrus sieboldi | native | ||
| Perciformes/Cottoidei | Liparidae | Pseudoliparis belyaevi | native | ||
| Gadiformes | Macrouridae | Pseudonezumia cetonuropsis | native | Japanese : Chidori-hige | |
| Gadiformes | Macrouridae | Pseudonezumia japonica | native | Japanese : Nihon-sokodara | |
| Ovalentaria/misc | Pseudochromidae | Pseudoplesiops rosae | native | Rose Island basslet | Japanese : Tanabatamegisu |
| Pleuronectiformes | Pleuronectidae | Pseudopleuronectes herzensteini | native | Yellow striped flounder | Japanese : Magarei |
| Pleuronectiformes | Pleuronectidae | Pseudopleuronectes obscurus | native | Japanese : Kurogarei | |
| Pleuronectiformes | Pleuronectidae | Pseudopleuronectes schrenki | native | Cresthead flounder | Japanese : Kurogashiragarei |
| Pleuronectiformes | Pleuronectidae | Pseudopleuronectes yokohamae | native | Marbled flounder | Japanese : Makogarei |
| Cypriniformes | Gobionidae | Pseudorasbora parva | native | Stone moroko | Japanese : Motsugo |
| Cypriniformes | Gobionidae | Pseudorasbora pugnax | native | ||
| Cypriniformes | Gobionidae | Pseudorasbora pumila | native | Moroco | Japanese : Shinai-motsugo |
| Cypriniformes | Acheilognathidae | Pseudorhodeus tanago | endemic | Tokyo bitterling | Japanese : Miyakotanago |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus arsius | native | Largetooth flounder | Japanese : Tenjikugarei |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus cinnamoneus | native | Cinnamon flounder | Japanese : Ganzôbirame |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus dupliciocellatus | native | Ocellated flounder | Japanese : Megarei |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus levisquamis | native | Japanese : Taiwan-ganzôbirame | |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus oculocirris | native | Japanese : Hera-ganzôbirame | |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus oligodon | native | Roughscale flounder | Japanese : Nanyôgarei |
| Pleuronectiformes | Paralichthyidae | Pseudorhombus pentophthalmus | native | Fivespot flounder | Japanese : Tama-ganzôbirame |
| Scombriformes | Chiasmodontidae | Pseudoscopelus sagamianus | native | Japanese : Kuro-bôzugisu | |
| Carcharhiniformes | Pseudotriakidae | Pseudotriakis microdon | native | False catshark | Japanese : Oshizame |
| Aulopiformes | Pseudotrichonotidae | Pseudotrichonotus altivelis | native | Japanese : Hotate-eso | |
| Perciformes/Cottoidei | Psychrolutidae | Psychrolutes paradoxus | native | Tadpole sculpin | Japanese : Uranaikajika |
| Perciformes/Cottoidei | Psychrolutidae | Psychrolutes phrictus | native | Blob sculpin | Japanese : Nyûdôkajika |
| Scombriformes | Bramidae | Pteraclis aesticola | native | Pacific fanfish | Japanese : Benten-uo |
| Eupercaria/misc | Labridae | Pteragogus aurigarius | native | Japanese : Ohaguro-bera | |
| Eupercaria/misc | Labridae | Pteragogus flagellifer | native | Cocktail wrasse | Japanese : Ohagurobera |
| Eupercaria/misc | Labridae | Pteragogus turdus | native | Thrush sneaky wrasse | Japanese : Tanuki-ohagurobera |
| Gobiiformes | Microdesmidae | Ptereleotris evides | native | Blackfin dartfish | Japanese : Kuroyurihaze |
| Gobiiformes | Microdesmidae | Ptereleotris grammica | native | Lined dartfish | Japanese : Suji-kuroyurihaze |
| Gobiiformes | Microdesmidae | Ptereleotris hanae | native | Blue hana goby | Japanese : Hanahaze |
| Gobiiformes | Microdesmidae | Ptereleotris heteroptera | native | Blacktail goby | Japanese : Oguro-kuroyurihaze |
| Gobiiformes | Microdesmidae | Ptereleotris microlepis | native | Blue gudgeon | Japanese : Itoman-kuroyurihaze |
| Gobiiformes | Microdesmidae | Ptereleotris monoptera | native | Lyre-tail dart-goby | |
| Gobiiformes | Microdesmidae | Ptereleotris zebra | native | Chinese zebra goby | Japanese : Zeburahaze |
| Eupercaria/misc | Caesionidae | Pterocaesio chrysozona | native | Goldband fusilier | Japanese : Takasago |
| Eupercaria/misc | Caesionidae | Pterocaesio digramma | native | Double-lined fusilier | Japanese : Nisen-takasago |
| Eupercaria/misc | Caesionidae | Pterocaesio marri | native | Marr's fusilier | |
| Eupercaria/misc | Caesionidae | Pterocaesio pisang | native | Banana fusilier | Japanese : Takasago |
| Eupercaria/misc | Caesionidae | Pterocaesio tile | native | Dark-banded fusilier | Japanese : Kumazasa-hanamuro |
| Gobiiformes | Gobiidae | Pterogobius elapoides | native | Japanese : Kinubari | |
| Gobiiformes | Gobiidae | Pterogobius virgo | native | Japanese : Nishikihaze | |
| Gobiiformes | Gobiidae | Pterogobius zacalles | native | Japanese : Ryugûhaze | |
| Gobiiformes | Gobiidae | Pterogobius zonoleucus | native | Japanese : Chagara | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pteroidichthys amboinensis | native | Ambon scorpionfish | Japanese : Tsunokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pteroidichthys noronhai | native | Noronha's scorpionfish | Japanese : Shinonome-tsunokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois antennata | native | Broadbarred firefish | Japanese : Nettai-minokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois lunulata | native | Luna lion fish | Japanese : Minokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois paucispinula | native | Japanese : Mizuhiki-minokasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois radiata | native | Radial firefish | Japanese : Kimiokoze |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois russelii | native | Plaintail turkeyfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Pterois volitans | native | Red lionfish | Japanese : Ominokasago |
| Myliobatiformes | Dasyatidae | Pteroplatytrygon violacea | native | Pelagic stingray | Japanese : Karasu-ei |
| Acropomatiformes | Hemerocoetidae | Pteropsaron evolans | native | Japanese : Hokaketoragisu | |
| Albuliformes | Albulidae | Pterothrissus gissu | native | Japanese gissu | Japanese : Gisu |
| Scombriformes | Bramidae | Pterycombus petersii | native | Prickly fanfish | Japanese : Ryûgû-no-hime |
| Siluriformes | Loricariidae | Pterygoplichthys disjunctivus | introduced | Vermiculated sailfin catfish | |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla cajorarori | native | Hyperostotic gurnard | |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla hemisticta | native | Blackspotted gurnard | Japanese : Sokohôbô |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla macrolepidota | native | Japanese : Uroko-sokohôbô | |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla macrorhynchus | native | Longnose gurnard | Japanese : Hananaga-sokohôbô |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla multiocellata | native | Antrorse spined gurnard | Japanese : Oni-sokohôbô |
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla multipunctata | native | ||
| Perciformes/Scorpaenoidei | Triglidae | Pterygotrigla ryukyuensis | native | Ryukyu gurnard | Japanese : Ryukyu-sokohôbô |
| Perciformes/Zoarcoidei | Ptilichthyidae | Ptilichthys goodei | native | Quillfish | Japanese : Hanegaji |
| Perciformes/Gasterosteoidei | Gasterosteidae | Pungitius modestus | native | Japanese : Kakure-tomiyo | |
| Perciformes/Gasterosteoidei | Gasterosteidae | Pungitius pungitius | native | Ninespine stickleback | Japanese : Ibara-tomiyo |
| Perciformes/Gasterosteoidei | Gasterosteidae | Pungitius sinensis | native | Amur stickleback | Japanese : Minami-tomiyo; Japanese : Tomiyo; |
| Perciformes/Gasterosteoidei | Gasterosteidae | Pungitius tymensis | native | Sakhalin stickleback | Japanese : Ezo-tomiyo |
| Cypriniformes | Gobionidae | Pungtungia herzi | native | Japanese : Mugitsuku | |
| Cypriniformes | Gobionidae | Pungtungia hilgendorfi | native | ||
| Cypriniformes | Gobionidae | Pungtungia shiraii | native | ||
| Perciformes/Zoarcoidei | Zoarcidae | Puzanovia rubra | native | Japanese : Akagenge | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis acares | native | Midget chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis alleni | native | Allen's chromis | Japanese : Onaga-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis amboinensis | native | Ambon chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis atripes | native | Dark-fin chromis | Japanese : Hireguro-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis delta | native | Deep reef chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis leucurus | native | Whitetail chromis | Japanese : Fukami-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis margaritifer | native | Bicolor chromis | Japanese : Shikoku-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis ovatiformis | native | Ovate chromis | Japanese : Maru-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis pacifica | native | Pacific bronze Chromis | |
| Ovalentaria/misc | Pomacentridae | Pycnochromis retrofasciatus | native | Black-bar chromis | Japanese : Kuroobi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Pycnochromis vanderbilti | native | Vanderbilt's chromis | Japanese : Hime-suzumedai |
| Ophidiiformes | Ophidiidae | Pycnocraspedum fulvum | native | Japanese : Ô-hime-itachiuo | |
| Ophidiiformes | Ophidiidae | Pycnocraspedum microlepis | native | Japanese : Hime-itachiuo | |
| Acanthuriformes | Pomacanthidae | Pygoplites diacanthus | native | Regal angelfish | Japanese : Nishikiyakko |
| Ophidiiformes | Carapidae | Pyramodon lindas | native | Blackedge pearlfish | |
| Ophidiiformes | Carapidae | Pyramodon ventralis | native | Pallid pearlfish | Japanese : Oni-kakureuo |
| Perciformes/Serranoidei | Anthiadidae | Pyronotanthias flavoguttatus | native | Yellow-spotted anthias | Japanese : Asahi-hanagoi |
| Perciformes/Serranoidei | Anthiadidae | Pyronotanthias lori | native | Lori's anthias | Japanese : Akaboshi-hanagoi |
| Perciformes/Serranoidei | Anthiadidae | Pyronotanthias parvirostris | native | Sunset anthias | |
| Perciformes/Serranoidei | Anthiadidae | Rabaulichthys suzukii | native | Japanese : Hokake-hanadai | |
| Carangiformes | Rachycentridae | Rachycentron canadum | native | Cobia | Japanese : Sugi |
| Perciformes/Cottoidei | Cottidae | Radulinopsis derjavini | native | Japanese : Yase-kajika | |
| Perciformes/Cottoidei | Cottidae | Radulinopsis taranetzi | native | Japanese : Kimadara-yase-kajika | |
| Eupercaria/misc | Lutjanidae | Randallichthys filamentosus | native | Randall's snapper | Japanese : Bake-akamutsu |
| Tetraodontiformes | Molidae | Ranzania laevis | native | Slender sunfish | Japanese : Kusabifugu |
| Scombriformes | Scombridae | Rastrelliger kanagurta | native | Indian mackerel | Japanese : Gurukuma |
| Perciformes/Scorpaenoidei | Platycephalidae | Ratabulus megacephalus | native | Japanese : Hanamegochi | |
| Gobiiformes | Gobiidae | Redigobius balteatus | native | Rhinohorn goby | |
| Gobiiformes | Gobiidae | Redigobius bikolanus | native | Speckled goby | Japanese : Hinahaze |
| Lampriformes | Regalecidae | Regalecus russellii | native | Oarfifsh | Japanese : Ryûgû-no-tsukai |
| Pleuronectiformes | Pleuronectidae | Reinhardtius hippoglossoides | native | Greenland halibut | Japanese : Karasugarei |
| Carangiformes | Echeneidae | Remora albescens | native | White suckerfish | Japanese : Shirokoban |
| Carangiformes | Echeneidae | Remora australis | native | Whalesucker | Japanese : Ôkoban |
| Carangiformes | Echeneidae | Remora brachyptera | native | Spearfish remora | Japanese : Kurokoban |
| Carangiformes | Echeneidae | Remora osteochir | native | Marlin sucker | Japanese : Hishikoban |
| Carangiformes | Echeneidae | Remora remora | native | Shark sucker | Japanese : Nagakoban |
| Callionymiformes | Callionymidae | Repomucenus huguenini | native | Huguenin's dragonet | Japanese : Yari-numeri |
| Callionymiformes | Callionymidae | Repomucenus ornatipinnis | native | Japanese ornate dragonet | Japanese : Seto-numeri |
| Callionymiformes | Callionymidae | Repomucenus virgis | native | Virgin dragonet | Japanese : Horo-numeri |
| Scombriformes | Gempylidae | Rexea bengalensis | native | Bengal escolar | |
| Scombriformes | Gempylidae | Rexea nakamurai | native | Nakamura's escolar | |
| Scombriformes | Gempylidae | Rexea prometheoides | native | Royal escolar | Japanese : Kagokamasu |
| Kurtiformes | Apogonidae | Rhabdamia gracilis | native | Luminous cardinalfish | Japanese : Sukashitenjikudai |
| Kurtiformes | Apogonidae | Rhabdamia novaluna | native | New-moon cardinalfish | Japanese : Shingetsu-sukashi-tenjikudai |
| Blenniiformes | Blenniidae | Rhabdoblennius nitidus | native | Barred-chin blenny | Japanese : Rôsokuginpo |
| Eupercaria/misc | Sparidae | Rhabdosargus sarba | native | Goldlined seabream | Japanese : Hedai |
| Stomiiformes | Stomiidae | Rhadinesthes decimus | native | Slender snaggletooth | Japanese : Yasetokagegisu |
| Perciformes/Cottoidei | Rhamphocottidae | Rhamphocottus richardsonii | native | Grunt sculpin | Japanese : Kuchibashikajika |
| Rhinopristiformes | Rhinidae | Rhina ancylostomus | native | Bowmouth guitarfish | Japanese : Shinonome sakatazame |
| Orectolobiformes | Rhincodontidae | Rhincodon typus | native | Whale shark | Japanese : Jinbeizame |
| Tetraodontiformes | Balistidae | Rhinecanthus abyssus | native | ||
| Tetraodontiformes | Balistidae | Rhinecanthus aculeatus | native | White-banded triggerfish | Japanese : Murasamemongara |
| Tetraodontiformes | Balistidae | Rhinecanthus rectangulus | native | Wedgetail triggerfish | Japanese : Tasukimongara |
| Tetraodontiformes | Balistidae | Rhinecanthus verrucosus | native | Blackbelly triggerfish | Japanese : Kurakakemongara |
| Rhinopristiformes | Rhinobatidae | Rhinobatos hynnicephalus | native | Angel fish | Japanese : Komon-sakatazame |
| Rhinopristiformes | Rhinobatidae | Rhinobatos schlegelii | native | Brown guitarfish | Japanese : Sakatazame |
| Chimaeriformes | Rhinochimaeridae | Rhinochimaera africana | native | Paddlenose chimaera | |
| Chimaeriformes | Rhinochimaeridae | Rhinochimaera pacifica | native | Pacific spookfish | Japanese : Tengu-ginzame |
| Gobiiformes | Gobiidae | Rhinogobius biwaensis | endemic | Japanese : Biwa-yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius brunneus | native | Amur goby | Japanese : Yoshinobori |
| Gobiiformes | Gobiidae | Rhinogobius flumineus | native | Japanese : Kawa-yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius giurinus | native | Japanese : Gokuraku-haze | |
| Gobiiformes | Gobiidae | Rhinogobius nagoyae | native | ||
| Gobiiformes | Gobiidae | Rhinogobius ogasawaraensis | native | Japanese : Ogasawara-yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius similis | native | Japanese : Gokuraku-haze | |
| Gobiiformes | Gobiidae | Rhinogobius telma | native | Japanese : Tokai-yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius tyoni | native | Japanese : Shimahire -yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius yaima | native | Japanese : Yaima-hira-yoshinobori | |
| Gobiiformes | Gobiidae | Rhinogobius yonezawai | native | Japanese : Kemmun-hira-yoshinobori | |
| Gobiesociformes | Gobiesocidae | Rhinolepadichthys geminus | native | Pacific doubleline clingfish | Japanese : Tasuji-umishida-ubauo |
| Perciformes/Cottoidei | Liparidae | Rhinoliparis barbulifer | native | Longnose snailfish | |
| Anguilliformes | Muraenidae | Rhinomuraena quaesita | native | Ribbon moray | Japanese : Hanahige-utsubo |
| Perciformes/Scorpaenoidei | Scorpaenidae | Rhinopias argoliba | native | Japanese : Namidakasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Rhinopias eschmeyeri | native | Eschmeyer's scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Rhinopias frondosa | native | Weedy scorpionfish | Japanese : Borokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Rhinopias xenops | native | Japanese : Nise-borokasago | |
| Myliobatiformes | Rhinopteridae | Rhinoptera javanica | native | Flapnose ray | Japanese : Ushibanatobi-ei |
| Rajiformes | Arhynchobatidae | Rhinoraja kujiensis | native | Dapple-bellied softnose skate | Japanese : Kujikasube |
| Rajiformes | Arhynchobatidae | Rhinoraja longicauda | native | White-bellied softnose skate | Japanese : Onagakasube |
| Rajiformes | Arhynchobatidae | Rhinoraja odai | native | Oda's skate | Japanese : Oda-ei |
| Pleuronectiformes | Soleidae | Rhinosolea microlepidota | native | Japanese : Tengu-ushinoshita | |
| Carcharhiniformes | Carcharhinidae | Rhizoprionodon acutus | native | Milk shark | Japanese : Hiragashira |
| Carcharhiniformes | Carcharhinidae | Rhizoprionodon oligolinx | native | Grey sharpnose shark | Japanese : Ankôzame |
| Cypriniformes | Acheilognathidae | Rhodeus atremius | native | Kyushu bitterling | Japanese : Kazetogetanago |
| Cypriniformes | Acheilognathidae | Rhodeus ocellatus | native | Rosy bitterling | Japanese : Nippon-bara-tanago; Japanese : Tairiku-baratanago; |
| Cypriniformes | Acheilognathidae | Rhodeus sciosemus | native | ||
| Cypriniformes | Acheilognathidae | Rhodeus smithii | endemic | Japanese : Nippon-baratanago | |
| Cypriniformes | Acheilognathidae | Rhodeus suigensis | native | Japanese : Suigen-zenitanago | |
| Perciformes/Zoarcoidei | Pholidae | Rhodymenichthys dolichogaster | native | Stippled gunnel | Japanese : Hakodateginpo |
| Gobiiformes | Rhyacichthyidae | Rhyacichthys aspro | native | Loach goby | Japanese : Tsubasahaze |
| Rhinopristiformes | Rhinidae | Rhynchobatus australiae | native | Bottlenose wedgefish | Japanese : Tongarisakata zame |
| Rhinopristiformes | Rhinidae | Rhynchobatus laevis | native | Smoothnose wedgefish | |
| Rhinopristiformes | Rhinidae | Rhynchobatus mononoke | endemic | Japanese wedgefish | Japanese : Mononoke-tongarisakatazame |
| Cypriniformes | Leuciscidae | Rhynchocypris lagowskii | native | Amur minnow | Japanese : Abura haya |
| Cypriniformes | Leuciscidae | Rhynchocypris mantschurica | native | Manchurian Lake minnow | |
| Cypriniformes | Leuciscidae | Rhynchocypris oxycephala | native | Chinese minnow | |
| Cypriniformes | Leuciscidae | Rhynchocypris percnura | native | Lake minnow | Japanese : Yachi ugui |
| Argentiniformes | Opisthoproctidae | Rhynchohyalus natalensis | native | Glasshead barreleye | Japanese : Yotsumenigisu |
| Centrarchiformes | Terapontidae | Rhynchopelates oxyrhynchus | native | Japanese : Shimaisaki | |
| Perciformes/Cottoidei | Cottidae | Ricuzenius nudithorax | native | Japanese : Munehadakajika | |
| Perciformes/Cottoidei | Cottidae | Ricuzenius pinetorum | native | Japanese : Matsukajika | |
| Acanthuriformes | Chaetodontidae | Roa haraguchiae | native | White-spine butterfyfsh | Japanese : Panda-genrokudai |
| Acanthuriformes | Chaetodontidae | Roa modesta | native | Brown-banded butterflyfish | Japanese : Genrokudai |
| Perciformes/Scorpaenoidei | Platycephalidae | Rogadius asper | native | Olive-tailed flathead | Japanese : Matsubagochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Rogadius patriciae | native | Black-banded flathead | |
| Beryciformes | Rondeletiidae | Rondeletia loricata | native | Redmouth whalefish | Japanese : Akachoki-kujira-uo |
| Aulopiformes | Scopelarchidae | Rosenblattichthys alatus | native | Winged pearleye | Japanese : Hirenaga-deme-eso |
| Alepocephaliformes | Alepocephalidae | Rouleina guentheri | native | Bordello slickhead | Japanese : Tanaka-sekitori-iwashi |
| Alepocephaliformes | Alepocephalidae | Rouleina watasei | native | Japanese : Sekitori-iwashi | |
| Tetraodontiformes | Monacanthidae | Rudarius ercodes | native | Whitespotted pygmy filefish | Japanese : Amimehagi |
| Tetraodontiformes | Monacanthidae | Rudarius excelsus | native | Diamond leatherjacket | |
| Scombriformes | Gempylidae | Ruvettus pretiosus | native | Oilfish | Japanese : Baramutsu |
| Perciformes/Uranoscopoidei | Pinguipedidae | Ryukyupercis gushikeni | native | Rosy grubfish | Japanese : Wani-toragisu |
| Perciformes/Serranoidei | Anthiadidae | Sacura margaritacea | native | Japanese : Sakuradai | |
| Gobiiformes | Gobiidae | Sagamia geneionema | native | Japanese : Sabihaze | |
| Alepocephaliformes | Platytroctidae | Sagamichthys abei | native | Shining tubeshoulder | Japanese : Haname-iwashi |
| Osmeriformes | Salangidae | Salangichthys microdon | native | Japanese icefish | Japanese : Shira-uo |
| Osmeriformes | Salangidae | Salanx ariakensis | native | Japanese : Ariake-shira-uo | |
| Blenniiformes | Blenniidae | Salarias alboguttatus | native | White-spotted blenny | |
| Blenniiformes | Blenniidae | Salarias fasciatus | native | Jewelled blenny | Japanese : Yaeyamaginpo |
| Blenniiformes | Blenniidae | Salarias guttatus | native | Breastspot blenny | |
| Blenniiformes | Blenniidae | Salarias luctuosus | native | Japanese : Shimaginpo | |
| Blenniiformes | Blenniidae | Salarias sinuosus | native | Fringelip blenny | Japanese : Hirenaga-kaeru-uo |
| Salmoniformes | Salmonidae | Salmo trutta | introduced | Sea trout | |
| Perciformes/Serranoidei | Epinephelidae | Saloptia powelli | native | Golden grouper | Japanese : Yamabukihata |
| Salmoniformes | Salmonidae | Salvelinus curilus | native | ||
| Salmoniformes | Salmonidae | Salvelinus fontinalis | introduced | Brook trout | Japanese : Kawamasu |
| Salmoniformes | Salmonidae | Salvelinus japonicus | endemic | Japanese : Kirikuchi char | |
| Salmoniformes | Salmonidae | Salvelinus leucomaenis | native | Whitespotted char | Japanese : Amemasu |
| Salmoniformes | Salmonidae | Salvelinus malma | native | Dolly varden | Japanese : Miyabe-iwana; Japanese : Oshorokoma; |
| Salmoniformes | Salmonidae | Salvelinus namaycush | introduced | Lake trout | |
| Pleuronectiformes | Samaridae | Samaris cristatus | native | Cockatoo righteye flounder | Japanese : Hatatategarei |
| Pleuronectiformes | Samaridae | Samariscus japonicus | native | Japanese : Tsukinowagarei | |
| Pleuronectiformes | Samaridae | Samariscus latus | native | Deep-body righteye flounder | Japanese : Tsumari-tsukinowagarei |
| Pleuronectiformes | Samaridae | Samariscus triocellatus | native | Three-spot righteye flounder | |
| Pleuronectiformes | Samaridae | Samariscus xenicus | native | Japanese : Ko-tsukinowagarei | |
| Cypriniformes | Gobionidae | Sarcocheilichthys biwaensis | endemic | Japanese : Abura-higai | |
| Cypriniformes | Gobionidae | Sarcocheilichthys variegatus | native | Japanese : Biwa-higai; Japanese : Kawa-higai; | |
| Scombriformes | Scombridae | Sarda orientalis | native | Striped bonito | Japanese : Hagatsuo |
| Clupeiformes | Dorosomatidae | Sardinella alcyone | native | Blueback Sardinella | Japanese : Shiosai-iwashi |
| Clupeiformes | Dorosomatidae | Sardinella electra | native | Island Sardinella | Japanese : Shimakaze-iwashi |
| Clupeiformes | Dorosomatidae | Sardinella lemuru | native | Bali sardinella | |
| Clupeiformes | Dorosomatidae | Sardinella melanura | native | Blacktip sardinella | |
| Clupeiformes | Dorosomatidae | Sardinella zunasi | native | Japanese sardinella | Japanese : Sappa |
| Clupeiformes | Alosidae | Sardinops sagax | native | Pacific sardine | Japanese : Sardinopa |
| Holocentriformes | Holocentridae | Sargocentron borodinoensis | native | Borodino soldierfish | |
| Holocentriformes | Holocentridae | Sargocentron caudimaculatum | native | Silverspot squirrelfish | Japanese : Kurakake-ebisu |
| Holocentriformes | Holocentridae | Sargocentron cornutum | native | Threespot squirrelfish | Japanese : Sumitsuki-kanoko |
| Holocentriformes | Holocentridae | Sargocentron diadema | native | Crown squirrelfish | Japanese : Niji-ebisu |
| Holocentriformes | Holocentridae | Sargocentron dorsomaculatum | native | Spotfin squirrelfish | Japanese : Bara-ebisu |
| Holocentriformes | Holocentridae | Sargocentron ensifer | native | Yellow-striped squirrelfish | Japanese : Hana-ebisu |
| Holocentriformes | Holocentridae | Sargocentron ittodai | native | Samurai squirrelfish | Japanese : Teri-ebisu |
| Holocentriformes | Holocentridae | Sargocentron melanospilos | native | Blackblotch squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron microstoma | native | Smallmouth squirrelfish | Japanese : Hime-ebisu |
| Holocentriformes | Holocentridae | Sargocentron praslin | native | Dark-striped squirrelfish | |
| Holocentriformes | Holocentridae | Sargocentron punctatissimum | native | Speckled squirrelfish | Japanese : Hoshi-ebisu |
| Holocentriformes | Holocentridae | Sargocentron rubrum | native | Redcoat | Japanese : Ayame-ebisu |
| Holocentriformes | Holocentridae | Sargocentron spiniferum | native | Sabre squirrelfish | Japanese : Togari-ebisu |
| Holocentriformes | Holocentridae | Sargocentron spinosissimum | native | North Pacific squirrelfish | Japanese : Ittoudai |
| Holocentriformes | Holocentridae | Sargocentron tiere | native | Blue lined squirrelfish | Japanese : Aosuji-ebisu |
| Holocentriformes | Holocentridae | Sargocentron tiereoides | native | Pink squirrelfish | Japanese : Sakura-ebisu |
| Holocentriformes | Holocentridae | Sargocentron violaceum | native | Violet squirrelfish | Japanese : Sumire-ebisu |
| Perciformes/Cottoidei | Agonidae | Sarritor frenatus | native | Sawback poacher | Japanese : Yase-tengu-tokubire |
| Perciformes/Cottoidei | Agonidae | Sarritor leptorhynchus | native | Longnose poacher | Japanese : Tengu-tokubire |
| Perciformes/Scorpaenoidei | Peristediidae | Satyrichthys laticeps | native | ||
| Perciformes/Scorpaenoidei | Peristediidae | Satyrichthys moluccensis | native | Black-finned armoured-gurnard | Japanese : Oki-kihoubou |
| Perciformes/Scorpaenoidei | Peristediidae | Satyrichthys rieffeli | native | Spotted armoured-gurnard | Japanese : Isokihôbô |
| Perciformes/Scorpaenoidei | Peristediidae | Satyrichthys welchi | native | Robust armoured-gurnard | Japanese : Hon-oki-kihoubou |
| Anguilliformes | Nettastomatidae | Saurenchelys fierasfer | native | Japanese : Ito-anago | |
| Aulopiformes | Synodontidae | Saurida elongata | native | Slender lizardfish | Japanese : Tokage-eso |
| Aulopiformes | Synodontidae | Saurida gracilis | native | Gracile lizardfish | Japanese : Madara-eso |
| Aulopiformes | Synodontidae | Saurida macrolepis | native | Japanese : Ma-eso | |
| Aulopiformes | Synodontidae | Saurida microlepis | native | ||
| Aulopiformes | Synodontidae | Saurida nebulosa | native | Clouded lizardfish | |
| Aulopiformes | Synodontidae | Saurida umeyoshii | native | Japanese : Kuro-eso | |
| Aulopiformes | Synodontidae | Saurida wanieso | native | Wanieso lizardfish | Japanese : Wani-eso |
| Perciformes/Scorpaenoidei | Peristediidae | Scalicus amiscus | native | Japanese : Higekihôbô | |
| Perciformes/Scorpaenoidei | Peristediidae | Scalicus engyceros | native | Japanese : Sokokihôbô | |
| Perciformes/Scorpaenoidei | Peristediidae | Scalicus hians | native | Japanese : Nanyôkihôbô | |
| Perciformes/Scorpaenoidei | Peristediidae | Scalicus quadratorostratus | native | Japanese : Soko-kihoubou | |
| Perciformes/Scorpaenoidei | Peristediidae | Scalicus serrulatus | native | Japanese : Togekihôbô | |
| Gobiiformes | Oxudercidae | Scartelaos histophorus | native | Walking goby | Japanese : Tokagehaze |
| Blenniiformes | Blenniidae | Scartella cristata | native | Molly miller | Japanese : Tategamiginpo |
| Eupercaria/misc | Scaridae | Scarus altipinnis | native | Filament-finned parrotfish | |
| Eupercaria/misc | Scaridae | Scarus chameleon | native | Chameleon parrotfish | |
| Eupercaria/misc | Scaridae | Scarus dimidiatus | native | Yellowbarred parrotfish | Japanese : Kawaribudai |
| Eupercaria/misc | Scaridae | Scarus festivus | native | Festive parrotfish | Japanese : Tsukinowabudai |
| Eupercaria/misc | Scaridae | Scarus forsteni | native | Forsten's parrotfish | |
| Eupercaria/misc | Scaridae | Scarus frenatus | native | Bridled parrotfish | Japanese : Amimebudai |
| Eupercaria/misc | Scaridae | Scarus fuscocaudalis | native | Darktail parrotfish | |
| Eupercaria/misc | Scaridae | Scarus ghobban | native | Blue-barred parrotfish | Japanese : Hibudai |
| Eupercaria/misc | Scaridae | Scarus globiceps | native | Globehead parrotfish | Japanese : Daidai-budai |
| Eupercaria/misc | Scaridae | Scarus hypselopterus | native | Yellowtail parrotfish | Japanese : Kibirebudai |
| Eupercaria/misc | Scaridae | Scarus niger | native | Dusky parrotfish | Japanese : Buchibudai |
| Eupercaria/misc | Scaridae | Scarus obishime | native | Japanese : Obishime | |
| Eupercaria/misc | Scaridae | Scarus oviceps | native | Darkcap parrotfish | Japanese : Hime-budai |
| Eupercaria/misc | Scaridae | Scarus ovifrons | native | Knobsnout parrotfish | Japanese : Aobudai |
| Eupercaria/misc | Scaridae | Scarus prasiognathos | native | Singapore parrotfish | Japanese : Nishikibudai |
| Eupercaria/misc | Scaridae | Scarus psittacus | native | Common parrotfish | Japanese : Ômubudai |
| Eupercaria/misc | Scaridae | Scarus quoyi | native | Quoy's parrotfish | Japanese : Remonbudai |
| Eupercaria/misc | Scaridae | Scarus rivulatus | native | Rivulated parrotfish | Japanese : Sujibudai |
| Eupercaria/misc | Scaridae | Scarus rubroviolaceus | native | Ember parrotfish | Japanese : Naga-budai |
| Eupercaria/misc | Scaridae | Scarus schlegeli | native | Yellowband parrotfish | Japanese : Obibudai |
| Eupercaria/misc | Scaridae | Scarus spinus | native | Greensnout parrotfish | Japanese : Shiro-obi-budai |
| Eupercaria/misc | Scaridae | Scarus tricolor | native | Tricolour parrotfish | Japanese : Ichimonji-budai |
| Eupercaria/misc | Scaridae | Scarus xanthopleura | native | Red parrotfish | Japanese : Akabudai |
| Acanthuriformes | Scatophagidae | Scatophagus argus | native | Spotted scat | Japanese : Kurohoshimanjûdai |
| Gobiiformes | Schindleriidae | Schindleria praematura | native | Schindler's fish | Japanese : Shirasu-uo |
| Gobiiformes | Gobiidae | Schismatogobius ampluvinculus | native | Japanese : Shima-esohaze | |
| Gobiiformes | Gobiidae | Schismatogobius marmoratus | native | Japanese : Kaeru-eso-haze | |
| Gobiiformes | Gobiidae | Schismatogobius roxasi | native | Japanese : Esohaze | |
| Gobiiformes | Gobiidae | Schismatogobius saurii | native | Japanese : Eso-haze | |
| Anguilliformes | Ophichthidae | Scolecenchelys aoki | native | Misaki worm eel | Japanese : Misaki-unagi; Japanese : Nihon-mimizuanago; |
| Anguilliformes | Ophichthidae | Scolecenchelys fuscapenis | native | ||
| Anguilliformes | Ophichthidae | Scolecenchelys fuscogularis | native | Dark throat worm eel | Japanese : Nodoguro-mimizu-anago |
| Anguilliformes | Ophichthidae | Scolecenchelys gymnota | native | Indo-Pacific slender worm-eel | Japanese : Mimizu-anago |
| Anguilliformes | Ophichthidae | Scolecenchelys iredalei | native | Coral worm eel | Japanese : Sango-mimizu-anago |
| Anguilliformes | Ophichthidae | Scolecenchelys macroptera | native | Narrow worm eel | Japanese : Kuri-mimizu-anago |
| Carcharhiniformes | Carcharhinidae | Scoliodon laticaudus | native | Spadenose shark | Japanese : Togari-ankôzame |
| Carcharhiniformes | Carcharhinidae | Scoliodon macrorhynchos | native | Pacific spadenose shark | |
| Eupercaria/misc | Nemipteridae | Scolopsis affinis | native | Peters' monocle bream | |
| Eupercaria/misc | Nemipteridae | Scolopsis bilineata | native | Two-lined monocle bream | Japanese : Futasuji-tamagashira |
| Eupercaria/misc | Nemipteridae | Scolopsis ciliata | native | Saw-jawed monocle bream | Japanese : Hakusen-tamagashira |
| Eupercaria/misc | Nemipteridae | Scolopsis japonica | native | Javanese monocle bream | Japanese : Taiwan-tamagashira |
| Eupercaria/misc | Nemipteridae | Scolopsis lineata | native | Striped monocle bream | Japanese : Yokosuji-tamagashira |
| Eupercaria/misc | Nemipteridae | Scolopsis monogramma | native | Monogrammed monocle bream | Japanese : Hime-tamagashira |
| Scombriformes | Scombridae | Scomber australasicus | native | Blue mackerel | Japanese : Marusaba |
| Scombriformes | Scombridae | Scomber japonicus | native | Chub mackerel | Japanese : Hirasaba |
| Carangiformes | Carangidae | Scomberoides commersonnianus | native | Talang queenfish | Japanese : Okuchi-Ikekatsuo |
| Carangiformes | Carangidae | Scomberoides lysan | native | Doublespotted queenfish | Japanese : Ikekatsuo |
| Carangiformes | Carangidae | Scomberoides tol | native | Needlescaled queenfish | Japanese : Minami-ikekatsuo |
| Scombriformes | Scombridae | Scomberomorus commerson | native | Narrow-barred Spanish mackerel | Japanese : Yokoshima-sawara |
| Scombriformes | Scombridae | Scomberomorus guttatus | native | Indo-Pacific king mackerel | Japanese : Taiwan-sawara |
| Scombriformes | Scombridae | Scomberomorus koreanus | native | Korean seerfish | Japanese : Hira-sawara |
| Scombriformes | Scombridae | Scomberomorus niphonius | native | Japanese Spanish mackerel | Japanese : Sawara |
| Scombriformes | Scombridae | Scomberomorus sinensis | native | Chinese seerfish | Japanese : Ushi-sawara |
| Scombriformes | Scombrolabracidae | Scombrolabrax heterolepis | native | Longfin escolar | Japanese : Mukashikurotachi |
| Acropomatiformes | Scombropidae | Scombrops boops | native | Gnomefish | Japanese : Mutsu |
| Acropomatiformes | Scombropidae | Scombrops gilberti | native | Japanese : Kuro-mutsu | |
| Aulopiformes | Scopelarchidae | Scopelarchus analis | native | Short fin pearleye | Japanese : Deme-eso-damashi |
| Myctophiformes | Neoscopelidae | Scopelengys tristis | native | Pacific blackchin | Japanese : Kurogo-iwashi |
| Beryciformes | Melamphaidae | Scopeloberyx opisthopterus | native | Japanese : Hime-tate-kabuto-uo | |
| Beryciformes | Melamphaidae | Scopeloberyx robustus | native | Longjaw bigscale | Japanese : Tate-kabuto-uo |
| Beryciformes | Melamphaidae | Scopeloberyx rossicus | native | ||
| Beryciformes | Melamphaidae | Scopelogadus mizolepis | native | Ragged bigscale | Japanese : Yoroiginme |
| Aulopiformes | Notosudidae | Scopelosaurus adleri | native | ||
| Aulopiformes | Notosudidae | Scopelosaurus harryi | native | Scaly paperbone | Japanese : Harii-fude-eso |
| Aulopiformes | Notosudidae | Scopelosaurus hoedti | native | Hoedt's waryfish | Japanese : Hikari-fude-eso |
| Aulopiformes | Notosudidae | Scopelosaurus mauli | native | Maul's waryfish | Japanese : Maoru-fude-eso |
| Aulopiformes | Notosudidae | Scopelosaurus smithii | native | Japanese : Fude-eso | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena brevispina | native | Japanese shortspined scorpionfish | Japanese : Kurenai-fusakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena hatizyoensis | native | Japanese : Hachijô-fusakasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena izensis | native | Izu scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena miostoma | native | Japanese : Kokuchi-fusakasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena neglecta | native | Japanese : Izukasago | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaena onaria | native | Western scorpionfish | Japanese : Fusakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes albaiensis | native | Longfingered scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes evides | native | Cheekspot scorpionfish | Japanese : Isokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes guamensis | native | Guam scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes hirsutus | native | Hairy scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes kelloggi | native | Kellogg's scorpionfish | Japanese : Guamukasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes minor | native | Minor scorpionfish | Japanese : Yubinagakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes parvipinnis | native | Lowfin scorpionfish | Japanese : Hime-sangokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes quadrispinosus | native | Fourspine scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenodes scaber | native | Pygmy scorpionfish | Japanese : Sangokasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis cirrosa | native | Weedy stingfish | Japanese : Onikasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis cotticeps | native | Sculpin scorpionfish | Japanese : Hime-satsuma-kasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis diabolus | native | False stonefish | Japanese : Satsumakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis macrochir | native | Flasher scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis neglecta | native | Yellowfin scorpionfish | Japanese : Toyo kasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis orientalis | native | ||
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis papuensis | native | Papuan scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis venosa | native | Raggy scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Scorpaenopsis vittapinna | native | Bandfin scorpionfish | |
| Anguilliformes | Muraenidae | Scuticaria okinawae | native | Shorttailed snake moray | |
| Carcharhiniformes | Scyliorhinidae | Scyliorhinus hachijoensis | native | Cinder cloudy catshark | Japanese : Fukami-torazame |
| Carcharhiniformes | Scyliorhinidae | Scyliorhinus torazame | native | Cloudy catshark | Japanese : Izu-hana-torazame; Japanese : Torazame; |
| Squaliformes | Somniosidae | Scymnodon ichiharai | native | Japanese velvet dogfish | Japanese : Ichihara-biroudozame |
| Carangiformes | Carangidae | Scyris indica | native | Indian threadfish | Japanese : Umazura-aji |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes cyanostigma | native | Yellowspotted scorpionfish | Japanese : Kasuri-fusakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes mauritiana | native | Spineblotch scorpionfish | |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes perplexa | native | Temperate scorpionfish | Japanese : Akamadara-fusakasago |
| Perciformes/Scorpaenoidei | Scorpaenidae | Sebastapistes tinkhami | native | Darkspotted scorpionfish | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes aleutianus | native | Rougheye rockfish | Japanese : Aramenuke |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes alutus | native | Pacific ocean perch | Japanese : Arasukamenuke |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes baramenuke | native | Japanese : Baramenuke | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes borealis | native | Shortraker rockfish | Japanese : Hireguromenuke |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes flammeus | native | Japanese : Sankômenuke | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes glaucus | native | Gray rockfish | Japanese : Kuromenuke |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes hubbsi | native | ||
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes ijimae | native | Japanese : Kôrai-kitsunemebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes inermis | native | Japanese : Mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes iracundus | native | Japanese : Ôsaga | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes itinus | native | Japanese : Yanagi-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes joyneri | native | Japanese : Togotto-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes kiyomatsui | native | Japanese : kataboshi-aka-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes longispinis | native | Japanese : Kôrai-yoroimebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes matsubarai | native | Japanese : Akôdai | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes melanostictus | native | Blackspotted rockfish | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes minor | native | Japanese : Akagaya | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes nivosus | native | Japanese : Gomasoi | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes nudus | native | Japanese : Akabuchi-murasoi; Japanese : Ōgon-murasoi; | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes oblongus | native | Japanese : Takenokomebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes owstoni | native | Japanese : Hatsume | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes pachycephalus | native | Japanese : Murasoi | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes schlegelii | native | Korean rockfish | Japanese : Kurosoi |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes scythropus | native | Japanese : Ukeguchi-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes steindachneri | native | Japanese : Yanaginomai | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes taczanowskii | native | Japanese : Ezo-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes thompsoni | native | Japanese : Usu-mebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes trivittatus | native | Japanese : Shimasoi | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes variabilis | native | Light dusky rockfish | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes ventricosus | native | ||
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes vulpes | native | Japanese : Kitsunemebaru | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes wakiyai | native | Japanese : Gayamodoki | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastes zonatus | native | ||
| Perciformes/Scorpaenoidei | Sebastidae | Sebastiscus albofasciatus | native | Japanese : Ayame-kasago | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastiscus marmoratus | native | False kelpfish | Japanese : Kasago |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastiscus tertius | native | Japanese : Ukkari-kasago | |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastolobus alascanus | native | Shortspine thornyhead | Japanese : Arasuka-kichiji |
| Perciformes/Scorpaenoidei | Sebastidae | Sebastolobus macrochir | native | Broadbanded thornyhead | Japanese : Kichiji |
| Carangiformes | Carangidae | Selar boops | native | Oxeye scad | |
| Carangiformes | Carangidae | Selar crumenophthalmus | native | Bigeye scad | Japanese : Me-aji |
| Carangiformes | Carangidae | Selaroides leptolepis | native | Yellowstripe scad | Japanese : Hosohira-aji |
| Perciformes/Serranoidei | Anthiadidae | Selenanthias analis | native | Pearl-spotted fairy basslet | Japanese : Sumitsuki-hanadai |
| Carangiformes | Carangidae | Seriola dumerili | native | Greater amberjack | Japanese : Kanpachi |
| Carangiformes | Carangidae | Seriola lalandi | native | Yellowtail amberjack | Japanese : Inada |
| Carangiformes | Carangidae | Seriola quinqueradiata | native | Japanese amberjack | Japanese : Buri |
| Carangiformes | Carangidae | Seriola rivoliana | native | Longfin yellowtail | Japanese : Hirenaga-kanpachi |
| Carangiformes | Carangidae | Seriolina nigrofasciata | native | Blackbanded trevally | Japanese : Aiburi |
| Perciformes/Serranoidei | Anthiadidae | Serranocirrhitus latus | native | Hawkfish anthias | Japanese : Hanagonbe |
| Anguilliformes | Serrivomeridae | Serrivomer sector | native | Sawtooth eel | Japanese : Nokoba-unagi |
| Perciformes/Scorpaenoidei | Setarchidae | Setarches guentheri | native | Channeled rockfish | Japanese : Shirokasago |
| Clupeiformes | Engraulidae | Setipinna tenuifilis | native | Common hairfin anchovy | |
| Gobiiformes | Gobiidae | Sicyopterus japonicus | native | Japanese : Bôzuhaze | |
| Gobiiformes | Gobiidae | Sicyopterus lagocephalus | native | Red-tailed goby | Japanese : Ruri-bōzuhaze |
| Gobiiformes | Gobiidae | Sicyopterus longifilis | native | Threadfin goby | |
| Gobiiformes | Gobiidae | Sicyopterus macrostetholepis | native | Japanese : Ruri-bôzuhaze | |
| Gobiiformes | Gobiidae | Sicyopus zosterophorus | native | Japanese : Aka-bôzuhaze | |
| Acanthuriformes | Siganidae | Siganus argenteus | native | Streamlined spinefoot | Japanese : Hana-aigo |
| Acanthuriformes | Siganidae | Siganus canaliculatus | native | White-spotted spinefoot | Japanese : Shimofuri-aigo |
| Acanthuriformes | Siganidae | Siganus corallinus | native | Blue-spotted spinefoot | Japanese : Sango-aigo |
| Acanthuriformes | Siganidae | Siganus fuscescens | native | Mottled spinefoot | Japanese : Aigo |
| Acanthuriformes | Siganidae | Siganus guttatus | native | Orange-spotted spinefoot | Japanese : Goma-aigo |
| Acanthuriformes | Siganidae | Siganus lineatus | native | Golden-lined spinefoot | |
| Acanthuriformes | Siganidae | Siganus puellus | native | Masked spinefoot | Japanese : Majiri-aigo |
| Acanthuriformes | Siganidae | Siganus punctatissimus | native | Peppered spinefoot | |
| Acanthuriformes | Siganidae | Siganus punctatus | native | Goldspotted spinefoot | Japanese : Buchi-aigo |
| Acanthuriformes | Siganidae | Siganus spinus | native | Little spinefoot | Japanese : Ami-aigo |
| Acanthuriformes | Siganidae | Siganus unimaculatus | native | Blotched foxface | |
| Acanthuriformes | Siganidae | Siganus vermiculatus | native | Vermiculated spinefoot | Japanese : Mushikui-aigo |
| Acanthuriformes | Siganidae | Siganus virgatus | native | Barhead spinefoot | Japanese : Hime-aigo |
| Stomiiformes | Gonostomatidae | Sigmops elongatus | native | Elongated bristlemouth fish | Japanese : Ô-yoko-eso |
| Stomiiformes | Gonostomatidae | Sigmops gracilis | native | Slender fangjaw | Japanese : Yoko-eso |
| Gobiiformes | Gobiidae | Silhouettea dotui | native | Japanese : Shiranuihaze | |
| Gobiiformes | Gobiidae | Silhouettea insinuans | native | Phantom goby | Japanese : Minami-shiranuihaze |
| Eupercaria/misc | Sillaginidae | Sillago aeolus | native | Oriental sillago | Japanese : Hoshi-gisu |
| Eupercaria/misc | Sillaginidae | Sillago japonica | native | Japanese sillago | Japanese : Shiro-gisu |
| Eupercaria/misc | Sillaginidae | Sillago parvisquamis | native | Small-scale sillago | Japanese : Aogisu |
| Eupercaria/misc | Sillaginidae | Sillago sihama | native | Silver sillago | Japanese : Kisu |
| Siluriformes | Siluridae | Silurus asotus | native | Amur catfish | Japanese : Namazu |
| Siluriformes | Siluridae | Silurus biwaensis | endemic | Eurasian catfish | Japanese : Biwako-ônamazu |
| Siluriformes | Siluridae | Silurus lithophilus | endemic | Japanese : Iwatoko-namazu | |
| Anguilliformes | Synaphobranchidae | Simenchelys parasitica | native | Snubnosed eel | Japanese : Kongô-anago |
| Kurtiformes | Apogonidae | Siphamia argentea | native | Silver siphonfish | |
| Kurtiformes | Apogonidae | Siphamia fuscolineata | native | Crown-of-thorns cardinalfish | |
| Kurtiformes | Apogonidae | Siphamia majimai | native | Striped siphonfish | Japanese : Majima-kuro-ishimochi |
| Kurtiformes | Apogonidae | Siphamia senoui | native | ||
| Kurtiformes | Apogonidae | Siphamia tubifer | native | Tubifer cardinalfish | Japanese : Hikari-ishimochi |
| Kurtiformes | Apogonidae | Siphamia tubulata | native | Siphonfish | |
| Gobiiformes | Gobiidae | Siphonogobius nue | native | Japanese : Nue-haze | |
| Ophidiiformes | Ophidiidae | Sirembo imberbis | native | Golden cusk | Japanese : Umidojô |
| Lophiiformes | Lophiidae | Sladenia zhui | native | ||
| Gobiiformes | Gobiidae | Smilosicyopus leprurus | native | Japanese : Kaeruhaze | |
| Perciformes/Scorpaenoidei | Tetrarogidae | Snyderina yamanokami | native | Japanese : Yamahime | |
| Perciformes/Zoarcoidei | Stichaeidae | Soldatovia polyactocephala | native | Japanese : Kita-fusa-ginpo | |
| Syngnathiformes | Syngnathidae | Solegnathus hardwickii | native | Hardwicke's pipefish | Japanese : Sumitsukiyôji |
| Pleuronectiformes | Soleidae | Soleichthys heterorhinos | native | Black-tip sole | Japanese : Sazanami-ushinoshita |
| Syngnathiformes | Solenostomidae | Solenostomus armatus | native | Armored pipefish | |
| Syngnathiformes | Solenostomidae | Solenostomus cyanopterus | native | Ghost pipefish | Japanese : Kamisori-uo |
| Syngnathiformes | Solenostomidae | Solenostomus leptosoma | native | Delicate ghostpipefish | |
| Syngnathiformes | Solenostomidae | Solenostomus paegnius | native | Roughsnout ghost pipefish | Japanese : Nokogiri-fûrai-uo |
| Syngnathiformes | Solenostomidae | Solenostomus paradoxus | native | Harlequin ghost pipefish | Japanese : Fûrai-uo |
| Lophiiformes | Ogcocephalidae | Solocisquama stellulata | native | Japanese : Iga-fûryû-uo | |
| Squaliformes | Somniosidae | Somniosus longus | native | Frog shark | Japanese : Kaeruzame |
| Squaliformes | Somniosidae | Somniosus pacificus | native | Pacific sleeper shark | Japanese : Ondenzame |
| Ophidiiformes | Ophidiidae | Spectrunculus grandis | native | Pudgy cuskeel | Japanese : Sokobôzu |
| Kurtiformes | Apogonidae | Sphaeramia nematoptera | native | Pajama cardinalfish | Japanese : Manjû-ishimochi |
| Kurtiformes | Apogonidae | Sphaeramia orbicularis | native | Orbiculate cardinalfish | Japanese : Hososuji-manjû-ishimochi |
| Tetraodontiformes | Tetraodontidae | Sphoeroides pachygaster | native | Blunthead puffer | Japanese : Yoritofugu |
| Carangaria/misc | Sphyraenidae | Sphyraena acutipinnis | native | Sharpfin barracuda | Japanese : Ôyamato-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena barracuda | native | Great barracuda | Japanese : Oni-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena flavicauda | native | Yellowtail barracuda | Japanese : Taiwan-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena forsteri | native | Bigeye barracuda | Japanese : Ôme-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena iburiensis | native | ||
| Carangaria/misc | Sphyraenidae | Sphyraena japonica | native | Japanese barracuda | Japanese : Yamato-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena obtusata | native | Obtuse barracuda | Japanese : Daruma-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena pinguis | native | Red barracuda | Japanese : Aka-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena putnamae | native | Sawtooth barracuda | Japanese : Ô-kamasu |
| Carangaria/misc | Sphyraenidae | Sphyraena qenie | native | Blackfin barracuda | |
| Carangaria/misc | Sphyraenidae | Sphyraena stellata | native | Yellow-striped barracuda | Japanese : Hoso-kamasu |
| Carcharhiniformes | Sphyrnidae | Sphyrna lewini | native | Scalloped hammerhead | Japanese : Aka-shumokuzame |
| Carcharhiniformes | Sphyrnidae | Sphyrna mokarran | native | Great hammerhead | Japanese : Hira-shumokuzame |
| Carcharhiniformes | Sphyrnidae | Sphyrna zygaena | native | Smooth hammerhead | Japanese : Shiro-shumokuzame |
| Gadiformes | Macrouridae | Spicomacrurus kuronumai | native | Kuronuma's whiptail | Japanese : Yaridara |
| Osmeriformes | Osmeridae | Spirinchus lanceolatus | endemic | Japanese : Shishamo | |
| Clupeiformes | Spratelloididae | Spratelloides delicatulus | native | Delicate round herring | Japanese : Minami-kibinago |
| Clupeiformes | Spratelloididae | Spratelloides gracilis | native | Silver-stripe round herring | Japanese : Bakajako |
| Blenniiformes | Clinidae | Springeratus xanthosoma | native | Indonesia weedfish | Japanese : Asahiginpo |
| Blenniiformes | Tripterygiidae | Springerichthys bapturus | native | Japanese blacktail triplefin | Japanese : Himeginpo |
| Cypriniformes | Gobionidae | Squalidus chankaensis | native | Khanka gudgeon | Japanese : Sugomoroko |
| Cypriniformes | Gobionidae | Squalidus gracilis | native | Japanese : Ito-moroko | |
| Cypriniformes | Gobionidae | Squalidus homozonus | native | ||
| Cypriniformes | Gobionidae | Squalidus japonicus | native | Japanese : Deme-moroko | |
| Squaliformes | Dalatiidae | Squaliolus aliae | native | Smalleye pygmy shark | Japanese : Tsuranaga-kobitozame |
| Squaliformes | Dalatiidae | Squaliolus laticaudus | native | Spined pygmy shark | Japanese : Oome-kobitozame |
| Gadiformes | Trachyrincidae | Squalogadus modificatus | native | Tadpole whiptail | Japanese : Bakedara |
| Perciformes/Cottoidei | Liparidae | Squaloliparis dentatus | native | Japanese : Ooban-konnyakuuo | |
| Squaliformes | Squalidae | Squalus blainville | native | Longnose spurdog | Japanese : Hiretakatsunozame |
| Squaliformes | Squalidae | Squalus brevirostris | native | ||
| Squaliformes | Squalidae | Squalus formosus | native | Taiwan spurdog | Japanese : Hiretaka-tsunozame |
| Squaliformes | Squalidae | Squalus japonicus | native | Japanese spurdog | Japanese : Togari-tsunozame |
| Squaliformes | Squalidae | Squalus megalops | native | Shortnose spurdog | Japanese : Tsumari-tsuno zame |
| Squaliformes | Squalidae | Squalus mitsukurii | native | Shortspine spurdog | Japanese : Futo-tsunozame |
| Squaliformes | Squalidae | Squalus shiraii | endemic | Shirai's spurdog | Japanese : Hiretaka-tsunozame |
| Squaliformes | Squalidae | Squalus suckleyi | native | Pacific spiny dogfish | Japanese : Abura-tsunozame |
| Squatiniformes | Squatinidae | Squatina formosa | native | Taiwan angleshark | English : Taiwan-korozame |
| Squatiniformes | Squatinidae | Squatina japonica | native | Japanese angelshark | Japanese : Kasuzame |
| Squatiniformes | Squatinidae | Squatina nebulosa | native | Clouded angelshark | Japanese : Korozame |
| Ovalentaria/misc | Opistognathidae | Stalix histrio | native | Harlequin jawfish | Japanese : Kaeru-amadai |
| Ovalentaria/misc | Opistognathidae | Stalix toyoshio | native | Japanese : Kibire-kaeruamadai | |
| Blenniiformes | Blenniidae | Stanulus talboti | native | Talbot's blenny | Japanese : Tsumariginpo |
| Ovalentaria/misc | Pomacentridae | Stegastes albifasciatus | native | Whitebar gregory | Japanese : Kiobi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Stegastes lacrymatus | native | Whitespotted devil | Japanese : Rurihoshi-suzumedai |
| Ovalentaria/misc | Pomacentridae | Stegastes nigricans | native | Dusky farmerfish | Japanese : Kurosora-suzumedai |
| Ovalentaria/misc | Pomacentridae | Stegastes punctatus | native | Blunt snout gregory | Japanese : Hananaga-suzumedai |
| Orectolobiformes | Stegostomatidae | Stegostoma tigrinum | native | Zebra shark | Japanese : Torafuzame |
| Perciformes/Cottoidei | Cottidae | Stelgistrum stejnegeri | native | Japanese : Ottoseikajika | |
| Anguilliformes | Serrivomeridae | Stemonidium hypomelas | native | Black serrivomerid eel | Japanese : Hime-nokoba-unagi |
| Aulopiformes | Paralepididae | Stemonosudis rothschildi | native | Rothschild's barracudina | Japanese : Kuranose-name-hadaka |
| Myctophiformes | Myctophidae | Stenobrachius leucopsarus | native | Northern lampfish | Japanese : Kohire-hadaka |
| Myctophiformes | Myctophidae | Stenobrachius nannochir | native | Garnet lanternfish | Japanese : Sekki-hadaka |
| Gobiiformes | Gobiidae | Stenogobius genivittatus | native | Chinstripe goby | Japanese : Tanekawahaze |
| Gobiiformes | Gobiidae | Stenogobius ophthalmoporus | native | Japanese : Dôkehaze | |
| Tetraodontiformes | Monacanthidae | Stephanolepis cirrhifer | native | Threadsail filefish | Japanese : Kawahagi |
| Acropomatiformes | Stereolepididae | Stereolepis doederleini | native | Striped giant seabass | Japanese : Ôkuchi-ishinagi |
| Acropomatiformes | Stereolepididae | Stereolepis gigas | native | Giant seabass | Japanese : Kokuchi-ishinagi |
| Stomiiformes | Sternoptychidae | Sternoptyx diaphana | native | Diaphanous hatchet fish | Japanese : Mune-eso |
| Stomiiformes | Sternoptychidae | Sternoptyx obscura | native | Japanese : Obi-mune-eso | |
| Stomiiformes | Sternoptychidae | Sternoptyx pseudobscura | native | Highlight hatchetfish | Japanese : Mune-eso-modoki |
| Eupercaria/misc | Labridae | Stethojulis bandanensis | native | Red shoulder wrasse | Japanese : Aka-obibera |
| Eupercaria/misc | Labridae | Stethojulis interrupta | native | Cutribbon wrasse | Japanese : Kaminaribera |
| Eupercaria/misc | Labridae | Stethojulis maculata | native | Japanese : Sumitsuki-kaminaribera | |
| Eupercaria/misc | Labridae | Stethojulis strigiventer | native | Three-ribbon wrasse | Japanese : Harasujibera |
| Eupercaria/misc | Labridae | Stethojulis terina | native | Japanese : Kaminaribera | |
| Eupercaria/misc | Labridae | Stethojulis trilineata | native | Three-lined rainbowfish | Japanese : Onibera |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeopsis epallax | native | Japanese : Ame-gaji | |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeopsis nana | native | Japanese : Gomaginpo | |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeus fuscus | native | Japanese : Tsuchi-gaji | |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeus grigorjewi | native | Japanese : Nagazuka | |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeus nozawae | native | Japanese : Tauegaji | |
| Perciformes/Zoarcoidei | Stichaeidae | Stichaeus ochriamkini | native | ||
| Gobiiformes | Gobiidae | Stiphodon alcedo | native | ||
| Gobiiformes | Gobiidae | Stiphodon atropurpureus | native | Japanese : Konteri-bōzuhaze | |
| Gobiiformes | Gobiidae | Stiphodon elegans | native | Japanese : Hayase-bôzuhaze; Japanese : Nanyô-bôzuhaze; | |
| Gobiiformes | Gobiidae | Stiphodon imperiorientis | native | Japanese : Hayase-bōzuhaze | |
| Gobiiformes | Gobiidae | Stiphodon multisquamus | native | Japanese : Torafu-bouzu-haze | |
| Gobiiformes | Gobiidae | Stiphodon niraikanaiensis | native | ||
| Gobiiformes | Gobiidae | Stiphodon percnopterygionus | native | ||
| Perciformes/Cottoidei | Cottidae | Stlengis distoechus | native | Japanese : Kushikajika-modoki | |
| Perciformes/Cottoidei | Cottidae | Stlengis misakia | native | Japanese : Urokokajika | |
| Perciformes/Cottoidei | Cottidae | Stlengis osensis | native | Japanese : Kushikajika | |
| Clupeiformes | Engraulidae | Stolephorus balinensis | native | Great anchovy | Japanese : Indo-ainokoiwashi |
| Clupeiformes | Engraulidae | Stolephorus mercurius | native | Mercury anchovy | Japanese : Yaeyama-ainokoiwashi |
| Stomiiformes | Stomiidae | Stomias affinis | native | Günther's boafish | Japanese : Wanitokagegisu |
| Stomiiformes | Stomiidae | Stomias longibarbatus | native | Longbarb scaly dragonfish | Japanese : Hoso-wanitokagegisu |
| Stomiiformes | Stomiidae | Stomias nebulosus | native | Alcock's boafish | Japanese : Yoroihoshi-eso |
| Gobiiformes | Gobiidae | Stonogobiops pentafasciatus | native | Japanese : Kitsuneme-neji | |
| Gobiiformes | Gobiidae | Stonogobiops xanthorhinicus | native | Yellownose prawn-goby | Japanese : Nejirinbô |
| Gobiiformes | Gobiidae | Stonogobiops yasha | native | Orange-striped shrimpgoby | |
| Beloniformes | Belonidae | Strongylura anastomella | native | Japanese : Datsu | |
| Beloniformes | Belonidae | Strongylura incisa | native | Reef needlefish | Japanese : Ryukyu-datsu |
| Anguilliformes | Muraenidae | Strophidon sathete | native | Slender giant moray | Japanese : Onaga-utsubo |
| Eupercaria/misc | Labridae | Suezichthys arquatus | native | Rainbow slender wrasse | |
| Eupercaria/misc | Labridae | Suezichthys gracilis | native | Slender wrasse | Japanese : Itobera |
| Eupercaria/misc | Labridae | Suezichthys notatus | native | Northern rainbow wrasse | Japanese : Mon-itobera |
| Eupercaria/misc | Labridae | Suezichthys soelae | native | Soela wrasse | |
| Tetraodontiformes | Balistidae | Sufflamen bursa | native | Boomerang triggerfish | Japanese : Musumehagi |
| Tetraodontiformes | Balistidae | Sufflamen chrysopterum | native | Halfmoon triggerfish | Japanese : Tsumajiromongara |
| Tetraodontiformes | Balistidae | Sufflamen fraenatum | native | Masked triggerfish | Japanese : Meganehagi |
| Perciformes/Scorpaenoidei | Platycephalidae | Suggrundus meerdervoortii | native | Japanese : Megochi | |
| Perciformes/Scorpaenoidei | Platycephalidae | Sunagocia arenicola | native | Broadhead flathead | Japanese : Sunagochi |
| Perciformes/Scorpaenoidei | Platycephalidae | Sunagocia otaitensis | native | Fringelip flathead | |
| Gobiiformes | Gobiidae | Suruga fundicola | native | Japanese : Yamihaze | |
| Perciformes/Serranoidei | Grammistidae | Suttonia lineata | native | Freckleface podge | |
| Myctophiformes | Myctophidae | Symbolophorus californiensis | native | Bigfin lanternfish | Japanese : Naga-hadaka |
| Myctophiformes | Myctophidae | Symbolophorus evermanni | native | Evermann's lantern fish | Japanese : Magari-hadaka |
| Eupercaria/misc | Lutjanidae | Symphorichthys spilurus | native | Sailfin snapper | Japanese : Irezumi-fuedai |
| Eupercaria/misc | Lutjanidae | Symphorus nematophorus | native | Chinamanfish | Japanese : Itohiki-fuedai |
| Pleuronectiformes | Cynoglossidae | Symphurus hondoensis | native | Japanese : Hondo-ushinoshita | |
| Pleuronectiformes | Cynoglossidae | Symphurus leucochilus | native | ||
| Pleuronectiformes | Cynoglossidae | Symphurus longirostris | native | Long-snout tonguefish | Japanese : Hashinaga-Azumagare |
| Pleuronectiformes | Cynoglossidae | Symphurus orientalis | native | Japanese : Azumagarei | |
| Pleuronectiformes | Cynoglossidae | Symphurus oxyrhynchus | native | Sharpnose tonguefish | English : Sharpnose tonguefish |
| Pleuronectiformes | Cynoglossidae | Symphurus robustus | native | Robust tonguefish | English : Robust tonguefish |
| Pleuronectiformes | Cynoglossidae | Symphurus strictus | native | Blackbelly tonguesole | Japanese : Himo-ushinoshita |
| Pleuronectiformes | Cynoglossidae | Symphurus thermophilus | native | Western Pacific tonguefish | |
| Acropomatiformes | Symphysanodontidae | Symphysanodon katayamai | native | Yellowstripe slopefish | Japanese : Kawarihanadai |
| Acropomatiformes | Symphysanodontidae | Symphysanodon maunaloae | native | Longtailed slopefish | Japanese : Paraohanadai |
| Acropomatiformes | Synagropidae | Synagrops japonicus | native | Blackmouth splitfin | Japanese : Sumikui-uo |
| Perciformes/Scorpaenoidei | Synanceiidae | Synanceia verrucosa | native | Stonefish | Japanese : Oni-darumaokoze |
| Anguilliformes | Synaphobranchidae | Synaphobranchus affinis | native | Grey cutthroat | Japanese : Hora-anago |
| Anguilliformes | Synaphobranchidae | Synaphobranchus brevidorsalis | native | Shortdorsal cutthroat eel | Japanese : Sode-anago |
| Anguilliformes | Synaphobranchidae | Synaphobranchus kaupii | native | Kaup's arrowtooth eel | Japanese : Irako-anago |
| Callionymiformes | Callionymidae | Synchiropus altivelis | native | Highfin bigeye dragonet | Japanese : Beni-teguri |
| Callionymiformes | Callionymidae | Synchiropus corallinus | native | Exclamation point dragonet | Japanese : Sango-hanabi-numeri |
| Callionymiformes | Callionymidae | Synchiropus ijimai | native | Japanese dragonet | Japanese : Yamadori |
| Callionymiformes | Callionymidae | Synchiropus kiyoae | native | Kiyo's dragonet | Japanese : Hime-teguri |
| Callionymiformes | Callionymidae | Synchiropus morrisoni | native | Morrison's dragonet | Japanese : Sesoko-teguri |
| Callionymiformes | Callionymidae | Synchiropus moyeri | native | Moyer's dragonet | Japanese : Miyake-teguri |
| Callionymiformes | Callionymidae | Synchiropus ocellatus | native | Ocellated dragonet | Japanese : Kouwan-teguri |
| Callionymiformes | Callionymidae | Synchiropus rubrovinctus | native | Tiny Hawaiian dragonet | Japanese : Akaobi-koteguri |
| Callionymiformes | Callionymidae | Synchiropus splendidus | native | Mandarinfish | Japanese : Nishiki-teguri |
| Syngnathiformes | Syngnathidae | Syngnathoides biaculeatus | native | Alligator pipefish | Japanese : Togeyôji |
| Syngnathiformes | Syngnathidae | Syngnathus chihiroe | native | English : Deepwater pipefish | |
| Syngnathiformes | Syngnathidae | Syngnathus schlegeli | native | Seaweed pipefish | Japanese : Yôji-uo |
| Aulopiformes | Synodontidae | Synodus binotatus | native | Twospot lizardfish | Japanese : Niten-eso |
| Aulopiformes | Synodontidae | Synodus dermatogenys | native | Sand lizardfish | |
| Aulopiformes | Synodontidae | Synodus doaki | native | Arrowtooth lizardfish | |
| Aulopiformes | Synodontidae | Synodus fuscus | native | Japanese : Suna-eso | |
| Aulopiformes | Synodontidae | Synodus hoshinonis | native | Blackear lizardfish | Japanese : Hoshino-eso |
| Aulopiformes | Synodontidae | Synodus jaculum | native | Lighthouse lizardfish | Japanese : Oguro-eso |
| Aulopiformes | Synodontidae | Synodus kaianus | native | Gunther's lizardfish | Japanese : Hanatogo-eso |
| Aulopiformes | Synodontidae | Synodus lobeli | native | Lobel's lizardfish | Japanese : Aosuji-eso |
| Aulopiformes | Synodontidae | Synodus macrops | native | Triplecross lizardfish | Japanese : Chôchô-eso |
| Aulopiformes | Synodontidae | Synodus oculeus | native | Large-eye lizardfish | Japanese : Irezumi-ome-eso |
| Aulopiformes | Synodontidae | Synodus orientalis | native | Asian lizardfish | |
| Aulopiformes | Synodontidae | Synodus rubromarmoratus | native | Redmarbled lizardfish | |
| Aulopiformes | Synodontidae | Synodus ulae | native | Red lizard fish | |
| Aulopiformes | Synodontidae | Synodus variegatus | native | Variegated lizardfish | Japanese : Hitosuji-eso; Japanese : Minami-aka-eso; |
| Myctophiformes | Myctophidae | Taaningichthys bathyphilus | native | Deepwater lanternfish | Japanese : Hage-kuro-hadaka |
| Myctophiformes | Myctophidae | Taaningichthys minimus | native | Waistcoat lanternfish | Japanese : Kurohadaka |
| Myctophiformes | Myctophidae | Taaningichthys paurolychnus | native | Japanese : Chihiro-kuro-hadaka | |
| Siluriformes | Bagridae | Tachysurus aurantiacus | endemic | Japanese : Ariake-gibachi | |
| Siluriformes | Bagridae | Tachysurus nudiceps | native | Japanese : Gigi | |
| Stomiiformes | Stomiidae | Tactostoma macropus | native | Longfin dragonfish | Japanese : Hadaka-hotei-eso |
| Kurtiformes | Apogonidae | Taeniamia biguttata | native | Twinspot cardinalfish | Japanese : Futahoshi-atohikitenjikudai |
| Kurtiformes | Apogonidae | Taeniamia fucata | native | Orangelined cardinalfish | Japanese : Atohikitenjikudai-damashi; Japanese : Sumitsuki-atohikitenjikudai; |
| Kurtiformes | Apogonidae | Taeniamia kagoshimana | native | Japanese : Sumitsuki-atohiki-tenjikudai | |
| Kurtiformes | Apogonidae | Taeniamia zosterophora | native | Blackbelted cardinalfish | Japanese : Kuroobi-atohikitenjikudai |
| Perciformes/Scorpaenoidei | Scorpaenidae | Taenianotus triacanthus | native | Leaf scorpionfish | Japanese : Hadakahaokoze |
| Gobiiformes | Gobiidae | Taenioides anguillaris | native | Eel worm goby | |
| Gobiiformes | Gobiidae | Taenioides cirratus | native | Bearded worm goby | Japanese : Chi-warasubo |
| Gobiiformes | Gobiidae | Taenioides gracilis | native | Slender eel goby | |
| Gobiiformes | Gobiidae | Taenioides kentalleni | native | ||
| Gobiiformes | Gobiidae | Taenioides limicola | native | Japanese : Hige-warasubo | |
| Pleuronectiformes | Bothidae | Taeniopsetta ocellata | native | Indo-Pacific ocellated flounder | Japanese : Itohiki-ganzôbirame |
| Myliobatiformes | Dasyatidae | Taeniura lymma | native | Ribbontail stingray | |
| Myliobatiformes | Dasyatidae | Taeniurops meyeni | native | Round ribbontail ray | Japanese : Madara-ei |
| Tetraodontiformes | Tetraodontidae | Takifugu alboplumbeus | native | Japanese : Komon-damashi | |
| Tetraodontiformes | Tetraodontidae | Takifugu bimaculatus | native | Japanese : Futatsuboshi-fugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu chinensis | native | Japanese : Karasu | |
| Tetraodontiformes | Tetraodontidae | Takifugu chrysops | native | Japanese : Akamefugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu exascurus | native | Japanese : Mushifugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu flavidus | native | Yellowbelly pufferfish | Japanese : Sansaifugu |
| Tetraodontiformes | Tetraodontidae | Takifugu flavipterus | native | Fine Patterned Puffer | Japanese : Komon-fugu |
| Tetraodontiformes | Tetraodontidae | Takifugu niphobles | native | Japanese : Kusafugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu oblongus | native | Lattice blaasop | Japanese : Takifugu |
| Tetraodontiformes | Tetraodontidae | Takifugu obscurus | native | Obscure pufferfish | Japanese : Mefugu |
| Tetraodontiformes | Tetraodontidae | Takifugu pardalis | native | Japanese : Higanfugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu poecilonotus | native | Japanese : Komonfugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu porphyreus | native | Japanese : Ma-fugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu pseudommus | native | Japanese : Nameradamashi | |
| Tetraodontiformes | Tetraodontidae | Takifugu radiatus | native | Japanese : Nashifugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu reticularis | native | Japanese : Amime-fugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu rubripes | native | Japanese pufferfish | Japanese : Torafugu |
| Tetraodontiformes | Tetraodontidae | Takifugu snyderi | native | Japanese : Shōsai-fugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu stictonotus | native | Japanese : Gomafugu | |
| Tetraodontiformes | Tetraodontidae | Takifugu vermicularis | native | Purple puffer | Japanese : Shosaifugu |
| Tetraodontiformes | Tetraodontidae | Takifugu xanthopterus | native | Yellowfin pufferfish | Japanese : Shimafugu |
| Alepocephaliformes | Alepocephalidae | Talismania antillarum | native | Antillean smooth-head | Japanese : Nokoba-iwashi |
| Alepocephaliformes | Alepocephalidae | Talismania filamentosa | native | Japanese : Mizuhiki-iwashi | |
| Cypriniformes | Acheilognathidae | Tanakia lanceolata | native | Japanese : Yari-tanago | |
| Cypriniformes | Acheilognathidae | Tanakia limbata | native | Oily bitterling | Japanese : Aburabote |
| Cypriniformes | Acheilognathidae | Tanakia shimazui | native | ||
| Scombriformes | Bramidae | Taractes asper | native | Rough pomfret | Japanese : Tsurugi-echiopia |
| Scombriformes | Bramidae | Taractes rubescens | native | Pomfret | Japanese : Tsurugi-echiopia |
| Scombriformes | Bramidae | Taractichthys steindachneri | native | Sickle pomfret | Japanese : Hirejiro-manzai-uo |
| Perciformes/Zoarcoidei | Zoarcidae | Taranetzella lyoderma | native | Looseskin eelpout | |
| Myctophiformes | Myctophidae | Tarletonbeania crenularis | native | Blue lanternfish | |
| Myctophiformes | Myctophidae | Tarletonbeania taylori | native | North Pacific lanternfish | Japanese : Hokuyô-hadaka |
| Pleuronectiformes | Paralichthyidae | Tarphops elegans | native | Japanese : Yume-aramegarei | |
| Pleuronectiformes | Paralichthyidae | Tarphops oligolepis | native | Japanese : Aramegarei | |
| Perciformes/Cottoidei | Cottidae | Taurocottus bergii | native | Japanese : Kirikajika | |
| Ovalentaria/misc | Pomacentridae | Teixeirichthys jordani | native | Jordan's damsel | Japanese : Suji-suzumedai |
| Myliobatiformes | Dasyatidae | Telatrygon acutirostra | native | Japanese : Yajiri-ei | |
| Myliobatiformes | Dasyatidae | Telatrygon zugei | native | Pale-edged stingray | Japanese : Zugu-ei |
| Scombriformes | Trichiuridae | Tentoriceps cristatus | native | Crested hairtail | Japanese : Kanmuridachi |
| Centrarchiformes | Terapontidae | Terapon jarbua | native | Jarbua terapon | Japanese : Kotohiki |
| Centrarchiformes | Terapontidae | Terapon theraps | native | Largescaled terapon | Japanese : Hime-kotohiki |
| Eupercaria/misc | Labridae | Terelabrus dewapyle | native | Yellow-striped hogfish | Japanese : Kisuge-miyabi-bera |
| Eupercaria/misc | Labridae | Terelabrus rubrovittatus | native | White-striped hogfish | |
| Scombriformes | Tetragonuridae | Tetragonurus atlanticus | native | Bigeye squaretail | Japanese : Tsumari-doku-uroko-ibodai |
| Scombriformes | Tetragonuridae | Tetragonurus cuvieri | native | Smalleye squaretail | Japanese : Doku-uroko-ibodai |
| Carangiformes | Istiophoridae | Tetrapturus angustirostris | native | Shortbill spearfish | Japanese : Fûraikajiki |
| Perciformes/Scorpaenoidei | Tetrarogidae | Tetraroge barbata | native | Bearded roguefish | Japanese : Agohige-okoze |
| Perciformes/Scorpaenoidei | Tetrarogidae | Tetraroge nigra | native | Japanese : Higesori-okoze | |
| Torpediniformes | Torpedinidae | Tetronarce californica | native | Pacific electric ray | |
| Torpediniformes | Torpedinidae | Tetronarce tokionis | native | Trapezoid torpedo | Japanese : Yamato-shibire-ei |
| Tetraodontiformes | Ostraciidae | Tetrosomus concatenatus | native | Triangular boxfish | Japanese : Hamafugu |
| Tetraodontiformes | Ostraciidae | Tetrosomus gibbosus | native | Humpback turretfish | Japanese : Rakuda-hakofugu |
| Tetraodontiformes | Ostraciidae | Tetrosomus reipublicae | native | Smallspine turretfish | Japanese : Hamafugu |
| Eupercaria/misc | Labridae | Thalassoma amblycephalum | native | Blunthead wrasse | Japanese : Kogashirabera |
| Eupercaria/misc | Labridae | Thalassoma cupido | native | Japanese : Nishikibera | |
| Eupercaria/misc | Labridae | Thalassoma hardwicke | native | Sixbar wrasse | Japanese : Senasujibera |
| Eupercaria/misc | Labridae | Thalassoma jansenii | native | Jansen's wrasse | Japanese : Yansen-nishikibera |
| Eupercaria/misc | Labridae | Thalassoma lunare | native | Moon wrasse | Japanese : Otomebera |
| Eupercaria/misc | Labridae | Thalassoma lutescens | native | Green moon wrasse | Japanese : Yamabukibera |
| Eupercaria/misc | Labridae | Thalassoma purpureum | native | Surge wrasse | Japanese : Kinu-bera |
| Eupercaria/misc | Labridae | Thalassoma quinquevittatum | native | Fivestripe wrasse | Japanese : Hakobera |
| Eupercaria/misc | Labridae | Thalassoma trilobatum | native | Christmas wrasse | Japanese : Ryûgûbera |
| Tetraodontiformes | Monacanthidae | Thamnaconus hypargyreus | native | Lesser-spotted leatherjacket | |
| Tetraodontiformes | Monacanthidae | Thamnaconus modestoides | native | Modest filefish | Japanese : Kibirekawahagi |
| Tetraodontiformes | Monacanthidae | Thamnaconus modestus | native | Black scraper | Japanese : Umazurahagi |
| Tetraodontiformes | Monacanthidae | Thamnaconus multilineatus | native | Japanese : Sen-umazurahagi | |
| Tetraodontiformes | Monacanthidae | Thamnaconus septentrionalis | native | Greenfin horse-faced filefish | Japanese : Nankai-umazurahagi |
| Tetraodontiformes | Monacanthidae | Thamnaconus tessellatus | native | Japanese : Goishi-umadsura-hagi | |
| Clupeiformes | Engraulidae | Thrissina baelama | native | Baelama anchovy | Japanese : Ainoko iwashi |
| Clupeiformes | Engraulidae | Thrissina chefuensis | native | Chefoo thryssa | Japanese : Tairiku-katakuchi |
| Clupeiformes | Engraulidae | Thryssa hamiltonii | native | Hamilton's thryssa | |
| Scombriformes | Scombridae | Thunnus alalunga | native | Albacore | Japanese : Binchô |
| Scombriformes | Scombridae | Thunnus albacares | native | Yellowfin tuna | Japanese : Kihada |
| Scombriformes | Scombridae | Thunnus obesus | native | Bigeye tuna | Japanese : Mebachi |
| Scombriformes | Scombridae | Thunnus orientalis | native | Pacific bluefin tuna | |
| Scombriformes | Scombridae | Thunnus tonggol | native | Longtail tuna | Japanese : Koshinaga |
| Scombriformes | Gempylidae | Thyrsitoides marleyi | native | Black snoek | Japanese : Nagatachikamasu |
| Stomiiformes | Stomiidae | Thysanactis dentex | native | Broomfin dragonfish | Japanese : Mayakashi-hoshi-eso |
| Perciformes/Scorpaenoidei | Scorpaenidae | Thysanichthys crossotus | native | Japanese : Fundôkasago | |
| Perciformes/Scorpaenoidei | Platycephalidae | Thysanophrys chiltonae | native | Longsnout flathead | Japanese : Kuroshimagochi |
| Cichliformes | Cichlidae | Tilapia sparrmanii | introduced | Banded tilapia | |
| Perciformes/Cottoidei | Agonidae | Tilesina gibbosa | native | Japanese : Onishachi-uo | |
| Ophidiiformes | Bythitidae | Timorichthys angustus | native | Japanese : Reiyou-itachiuo | |
| Cypriniformes | Tincidae | Tinca tinca | introduced | Tench | |
| Gobiiformes | Gobiidae | Tomiyamichthys alleni | native | Allen's shrimpgoby | |
| Gobiiformes | Gobiidae | Tomiyamichthys lanceolatus | native | Lanceolate shrimpgoby | Japanese : Yajirihaze |
| Gobiiformes | Gobiidae | Tomiyamichthys oni | native | Monster shrimpgoby | Japanese : Onihaze |
| Gobiiformes | Gobiidae | Tomiyamichthys smithi | native | Smith's shrimpgoby | |
| Tetraodontiformes | Tetraodontidae | Torquigener brevipinnis | native | ||
| Tetraodontiformes | Tetraodontidae | Torquigener florealis | native | ||
| Tetraodontiformes | Tetraodontidae | Torquigener hypselogeneion | native | Orange-spotted toadfish | Japanese : Shippôfugu |
| Perciformes/Serranoidei | Anthiadidae | Tosana niwae | native | Threadtail anthias | Japanese : Himehanadai |
| Perciformes/Serranoidei | Anthiadidae | Tosanoides filamentosus | native | Japanese : Itohikihanadai | |
| Perciformes/Serranoidei | Anthiadidae | Tosanoides flavofasciatus | native | Japanese : Kishimahanadai | |
| Pleuronectiformes | Bothidae | Tosarhombus octoculatus | native | Japanese : Yatsumedarumagarei | |
| Carangaria/misc | Toxotidae | Toxotes jaculatrix | native | Banded archerfish | Japanese : Teppō-uo |
| Perciformes/Cottoidei | Cottidae | Trachidermus fasciatus | native | Roughskin sculpin | |
| Aulopiformes | Synodontidae | Trachinocephalus trachinus | native | Japanese : Oki-eso | |
| Carangiformes | Carangidae | Trachinotus baillonii | native | Small spotted dart | Japanese : Koban-aji |
| Carangiformes | Carangidae | Trachinotus blochii | native | Snubnose pompano | Japanese : Marukoban |
| Carangiformes | Carangidae | Trachinotus mookalee | native | Indian pompano | |
| Lampriformes | Trachipteridae | Trachipterus ishikawae | native | Slender ribbonfish | Japanese : Sakegashira |
| Lampriformes | Trachipteridae | Trachipterus trachypterus | native | Mediterranean dealfish | Japanese : Kurogasira-sakegashira |
| Gadiformes | Macrouridae | Trachonurus villosus | native | Furry whiptail | Japanese : Wata hige |
| Carangiformes | Carangidae | Trachurus japonicus | native | Japanese jack mackerel | Japanese : Ma-aji |
| Syngnathiformes | Syngnathidae | Trachyrhamphus bicoarctatus | native | Double-ended pipefish | Japanese : Wakayôji |
| Syngnathiformes | Syngnathidae | Trachyrhamphus longirostris | native | Straightstick pipefish | Japanese : Itohikiyôji |
| Syngnathiformes | Syngnathidae | Trachyrhamphus serratus | native | Japanese : Hifukiyôji | |
| Tetraodontiformes | Triacanthodidae | Triacanthodes anomalus | native | Japanese : Benikawamuki | |
| Tetraodontiformes | Triacanthodidae | Triacanthodes ethiops | native | Shortsnout spikefish | Japanese : Shima-benikawamuki |
| Tetraodontiformes | Triacanthidae | Triacanthus biaculeatus | native | Short-nosed tripodfish | Japanese : Gima |
| Carcharhiniformes | Carcharhinidae | Triaenodon obesus | native | Whitetip reef shark | Japanese : Nemuribuka |
| Carcharhiniformes | Triakidae | Triakis scyllium | native | Banded houndshark | Japanese : Dochizame |
| Scombriformes | Trichiuridae | Trichiurus japonicus | native | ||
| Scombriformes | Trichiuridae | Trichiurus lepturus | native | Largehead hairtail | Japanese : Tachinouo |
| Scombriformes | Trichiuridae | Trichiurus margarites | native | ||
| Gobiiformes | Trichonotidae | Trichonotus elegans | native | Long-rayed sand-diver | Japanese : Ryûgû-beraginpo |
| Gobiiformes | Trichonotidae | Trichonotus filamentosus | native | English : Sand diver | |
| Gobiiformes | Trichonotidae | Trichonotus setiger | native | Spotted sand-diver | Japanese : Beraginpo |
| Gobiiformes | Gobiidae | Tridentiger barbatus | native | Shokihaze goby | Japanese : Shôkihaze |
| Gobiiformes | Gobiidae | Tridentiger bifasciatus | native | Shimofuri goby | Japanese : Shimofuri-shimahaze |
| Gobiiformes | Gobiidae | Tridentiger brevispinis | native | Japanese : Numa-chichibu | |
| Gobiiformes | Gobiidae | Tridentiger kuroiwae | native | Japanese : Naganogori | |
| Gobiiformes | Gobiidae | Tridentiger nudicervicus | native | Japanese : Shiro-chichibu | |
| Gobiiformes | Gobiidae | Tridentiger obscurus | native | Dusky tripletooth goby | Japanese : Chichibu |
| Gobiiformes | Gobiidae | Tridentiger trigonocephalus | native | Chameleon goby | Japanese : Shimahaze |
| Perciformes/Cottoidei | Cottidae | Triglops dorothy | native | Dorothy's sculpin | |
| Perciformes/Cottoidei | Cottidae | Triglops jordani | native | Jordan's sculpin | Japanese : Karafutokajika |
| Perciformes/Cottoidei | Cottidae | Triglops pingelii | native | Ribbed sculpin | Japanese : Hokkyokukajika |
| Perciformes/Cottoidei | Cottidae | Triglops scepticus | native | Spectacled sculpin | Japanese : Mogamikajika |
| Squaliformes | Etmopteridae | Trigonognathus kabeyai | native | Viper dogfish | Japanese : Waniguchi-tsunozame |
| Gobiiformes | Gobiidae | Trimma albicaudatum | native | ||
| Gobiiformes | Gobiidae | Trimma caesiura | native | Caesiura pygmygoby | Japanese : Benihaze |
| Gobiiformes | Gobiidae | Trimma caudipunctatum | native | Spot-tailed pygmygoby | Japanese : Daitoku-benihaze |
| Gobiiformes | Gobiidae | Trimma caudomaculatum | native | Blotch-tailed pygmygoby | |
| Gobiiformes | Gobiidae | Trimma fasciatum | native | Yellow-banded pygmygoby | Japanese : Dokutsu-shima-benihaze |
| Gobiiformes | Gobiidae | Trimma flammeum | native | Flame pygmygoby | |
| Gobiiformes | Gobiidae | Trimma flavatrum | native | Wasp pygmygoby | Japanese : Hime-aogi-haze |
| Gobiiformes | Gobiidae | Trimma grammistes | native | Black-striped pygmygoby | Japanese : Ichimonji-haze |
| Gobiiformes | Gobiidae | Trimma hayashii | native | Four-eye pygmygoby | Japanese : Eri-hoshi-beni-haze |
| Gobiiformes | Gobiidae | Trimma imaii | native | Imai's pygmygoby | Japanese : Murasakizukin-benihaze |
| Gobiiformes | Gobiidae | Trimma kudoi | native | Kudo's pygmygoby | Japanese : Nagashime-benihaze |
| Gobiiformes | Gobiidae | Trimma macrophthalmus | native | Large-eyed pygmygoby | |
| Gobiiformes | Gobiidae | Trimma maiandros | native | Zigzag pygmygoby | |
| Gobiiformes | Gobiidae | Trimma marinae | native | Princess pygmygoby | |
| Gobiiformes | Gobiidae | Trimma matsunoi | native | Matsuno's pygmygoby | Japanese : Kashiwa-benihaze |
| Gobiiformes | Gobiidae | Trimma naudei | native | Naude's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma nomurai | native | Lilac pygmygoby | Japanese : Kataboshinishiki-benihaze |
| Gobiiformes | Gobiidae | Trimma okinawae | native | Orange-red pygmygoby | Japanese : Okinawa-benihaze |
| Gobiiformes | Gobiidae | Trimma sheppardi | native | Sheppard's pygmygoby | |
| Gobiiformes | Gobiidae | Trimma yanagitai | native | Brown pygmygoby | Japanese : Oni-benihaze |
| Gobiiformes | Gobiidae | Trimma yanoi | native | Pudgy pygmygoby | Japanese : Hotei-benihaze |
| Gobiiformes | Gobiidae | Trimma yoshinoi | native | Yoshino's pygmygoby | Japanese : Ukibenihaze |
| Gobiiformes | Gobiidae | Trimmatom pharus | native | Lifehouse dwarfgoby | |
| Tetraodontiformes | Triodontidae | Triodon macropterus | native | Threetooth puffer | Japanese : Uchiwafugu |
| Perciformes/Serranoidei | Epinephelidae | Triso dermopterus | native | Oval grouper | Japanese : Tobihata |
| Gobiiformes | Gobiidae | Trypauchenopsis intermedia | native | Bearded Eel Goby | |
| Gobiiformes | Gobiidae | Tryssogobius colini | native | Colin's fairygoby | Japanese : Moegi-haze |
| Carangiformes | Carangidae | Turrum coeruleopinnatum | native | Coastal trevally | Japanese : Kii-hira-aji |
| Carangiformes | Carangidae | Turrum fulvoguttatum | native | Yellowspotted trevally | Japanese : Hoshi-kaiwari |
| Carangiformes | Carangidae | Turrum gymnostethus | native | Bludger | Japanese : Andaman-aji |
| Tetraodontiformes | Triacanthodidae | Tydemania navigatoris | native | Fleshy-lipped spikefish | Japanese : Sokokawamuki |
| Beloniformes | Belonidae | Tylosurus crocodilus | native | Hound needlefish | Japanese : Okizayori |
| Beloniformes | Belonidae | Tylosurus melanotus | native | Keeljaw needlefish | Japanese : Tenjiku-datsu |
| Blenniiformes | Tripterygiidae | Ucla xenogrammus | native | Largemouth triplefin | |
| Aulopiformes | Paralepididae | Uncisudis posteropelvis | native | ||
| Mulliformes | Mullidae | Upeneus elongatus | native | Elongate goatfish | Japanese : Iwanaga-himeji |
| Mulliformes | Mullidae | Upeneus guttatus | native | Twotone goatfish | |
| Mulliformes | Mullidae | Upeneus heterospinus | native | Variedspine goatfish | |
| Mulliformes | Mullidae | Upeneus itoui | native | Itou's goatfish | Japanese : Sakuya-himeji |
| Mulliformes | Mullidae | Upeneus japonicus | native | Japanese goatfish | Japanese : Himeji |
| Mulliformes | Mullidae | Upeneus moluccensis | native | Goldband goatfish | Japanese : Kisuji-himeji |
| Mulliformes | Mullidae | Upeneus quadrilineatus | native | Fourstripe goatfish | Japanese : Yosuji-himeji |
| Mulliformes | Mullidae | Upeneus subvittatus | native | Deepwater goatfish | Japanese : Yoko-himeji |
| Mulliformes | Mullidae | Upeneus sulphureus | native | Sulphur goatfish | Japanese : Mebuto-kandari |
| Mulliformes | Mullidae | Upeneus sundaicus | native | Ochre-banded goatfish | |
| Mulliformes | Mullidae | Upeneus taeniopterus | native | Bandtail goatfish | Japanese : Shirogane-himeji |
| Mulliformes | Mullidae | Upeneus tragula | native | Freckled goatfish | Japanese : Yome-himeji |
| Mulliformes | Mullidae | Upeneus vittatus | native | Striped goatfish | Japanese : Minami-himeji |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus bicinctus | native | Marbled stargazer | Japanese : Megane uo |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus chinensis | native | ||
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus japonicus | native | Japanese : Mishima-okoze | |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus sulphureus | native | Whitemargin stargazer | |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus tosae | native | Japanese : Yagimishima | |
| Perciformes/Uranoscopoidei | Uranoscopidae | Uranoscopus turbisquamatus | native | Japanese : Kasuri-mishima | |
| Carangiformes | Carangidae | Uraspis helvola | native | Whitetongue jack | Japanese : Okiaji |
| Carangiformes | Carangidae | Uraspis uraspis | native | Whitemouth jack | Japanese : Indo-okiaji |
| Syngnathiformes | Syngnathidae | Urocampus nanus | native | Barbed pipefish | Japanese : Okuyôji |
| Anguilliformes | Congridae | Uroconger lepturus | native | Slender conger | Japanese : Ai-anago |
| Myliobatiformes | Urolophidae | Urolophus aurantiacus | native | Sepia stingray | Japanese : Hirata-ei |
| Anguilliformes | Muraenidae | Uropterygius hades | native | ||
| Anguilliformes | Muraenidae | Uropterygius macrocephalus | native | Needle-tooth moray | Japanese : Hoshi-kikai-utsubo |
| Anguilliformes | Muraenidae | Uropterygius marmoratus | native | Marbled reef-eel | Japanese : Shizuku-kikai-utsubo |
| Anguilliformes | Muraenidae | Uropterygius micropterus | native | Tidepool snake moray | Japanese : Ami-kikai-utsubo |
| Anguilliformes | Muraenidae | Uropterygius nagoensis | native | Nago snakemoray | Japanese : Nago-kikai-utsubo |
| Perciformes/Scorpaenoidei | Scorpaenidae | Ursinoscorpaenopsis kitai | native | Japanese : Kuma-kasago | |
| Gobiiformes | Gobiidae | Valenciennea helsdingenii | native | Twostripe goby | Japanese : Kuroitohaze |
| Gobiiformes | Gobiidae | Valenciennea longipinnis | native | Long-finned goby | Japanese : Sazanamihaze |
| Gobiiformes | Gobiidae | Valenciennea muralis | native | Mural goby | |
| Gobiiformes | Gobiidae | Valenciennea parva | native | Parva goby | |
| Gobiiformes | Gobiidae | Valenciennea puellaris | native | Maiden goby | Japanese : Otomehaze |
| Gobiiformes | Gobiidae | Valenciennea sexguttata | native | Sixspot goby | Japanese : Mizutamahaze |
| Gobiiformes | Gobiidae | Valenciennea strigata | native | Blueband goby | Japanese : Akahachihaze |
| Gobiiformes | Gobiidae | Valenciennea wardii | native | Ward's sleeper | Japanese : Sasahaze |
| Gobiiformes | Gobiidae | Valenciennea yanoi | native | Japanese : Kiito-haze | |
| Stomiiformes | Sternoptychidae | Valenciennellus tripunctulatus | native | Constellationfish | Japanese : Hoshi-eso |
| Gobiiformes | Gobiidae | Vanderhorstia ambanoro | native | Ambanoro prawn-goby | Japanese : Shima-orihaze |
| Gobiiformes | Gobiidae | Vanderhorstia auropunctata | native | Japanese : Kirakirahaze | |
| Gobiiformes | Gobiidae | Vanderhorstia cyanolineata | native | Japanese : Aosujiyatsushi-haze | |
| Gobiiformes | Gobiidae | Vanderhorstia fulvopelvis | native | Japanese : Himeyatsushi-haze | |
| Gobiiformes | Gobiidae | Vanderhorstia hiramatsui | native | Japanese : Kuroerikanoko-haze | |
| Gobiiformes | Gobiidae | Vanderhorstia kizakura | native | Japanese : Kizakura-haze | |
| Gobiiformes | Gobiidae | Vanderhorstia macropteryx | native | Bigfin shrimpgoby | |
| Gobiiformes | Gobiidae | Vanderhorstia mertensi | native | Mertens' prawn-goby | Japanese : Kusahaze |
| Gobiiformes | Gobiidae | Vanderhorstia ornatissima | native | Ornate prawn-goby | Japanese : Yatsushihaze |
| Gobiiformes | Gobiidae | Vanderhorstia papilio | native | Butterfly shrimpgoby | Japanese : yano susobiki-haze |
| Gobiiformes | Gobiidae | Vanderhorstia phaeosticta | native | Yellowfoot shrimpgoby | |
| Gobiiformes | Gobiidae | Vanderhorstia puncticeps | native | Japanese : Ho'obeni-otohime-haze | |
| Gobiiformes | Gobiidae | Vanderhorstia rapa | native | Japanese : Nanohanafubuki-haze | |
| Perciformes/Serranoidei | Epinephelidae | Variola albimarginata | native | White-edged lyretail | Japanese : Ojiro-barahata |
| Perciformes/Serranoidei | Epinephelidae | Variola louti | native | Yellow-edged lyretail | Japanese : Bara-hata |
| Lampriformes | Veliferidae | Velifer hypselopterus | native | Sailfin velifer | Japanese : Kusa-aji |
| Perciformes/Cottoidei | Cottidae | Vellitor centropomus | native | Japanese : Sui | |
| Perciformes/Cottoidei | Cottidae | Vellitor minutus | native | Japanese : Hime-sui | |
| Anguilliformes | Nettastomatidae | Venefica proboscidea | native | Whipsnout sorcerer | |
| Anguilliformes | Nettastomatidae | Venefica tentaculata | native | Japanese : Kiseru-kuzu-anago | |
| Gadiformes | Macrouridae | Ventrifossa fusca | native | Japanese : Karasu-hige | |
| Gadiformes | Macrouridae | Ventrifossa garmani | native | Sagami grenadier | Japanese : Sagami-sokodara |
| Gadiformes | Macrouridae | Ventrifossa longibarbata | native | Japanese : Okina-hige | |
| Gadiformes | Macrouridae | Ventrifossa macroptera | native | Palau grenadier | Japanese : Parao-sokodara |
| Gadiformes | Macrouridae | Ventrifossa misakia | native | Misaki grenadier | Japanese : Misaki-sokodara |
| Gadiformes | Macrouridae | Ventrifossa nigrodorsalis | native | Spinaker grenadier | Japanese : Homaehige |
| Gadiformes | Macrouridae | Ventrifossa rhipidodorsalis | native | Japanese : Homae-hige | |
| Gadiformes | Macrouridae | Ventrifossa saikaiensis | native | ||
| Pleuronectiformes | Pleuronectidae | Verasper moseri | native | Barfin flounder | Japanese : Matsukawa |
| Pleuronectiformes | Pleuronectidae | Verasper variegatus | native | Spotted halibut | Japanese : Hoshigarei |
| Acropomatiformes | Malakichthyidae | Verilus pacificus | native | Japanese : Bakemutsu | |
| Kurtiformes | Apogonidae | Verulux cypselurus | native | Swallowtail cardinalfish | Japanese : Kurosuji-sukashitenjikudai |
| Stomiiformes | Phosichthyidae | Vinciguerria attenuata | native | Slender lightfish | Japanese : Uki-eso |
| Stomiiformes | Phosichthyidae | Vinciguerria nimbaria | native | Oceanic lightfish | Japanese : Yabe-uki-eso |
| Stomiiformes | Phosichthyidae | Vinciguerria poweriae | native | Power's deep-water bristle-mouth fish | Japanese : Oki-uki-eso |
| Eupercaria/misc | Lethrinidae | Wattsia mossambica | native | Mozambique large-eye bream | Japanese : Koke-nokogiri |
| Eupercaria/misc | Labridae | Wetmorella nigropinnata | native | Sharpnose wrasse | Japanese : Hashinagabera |
| Argentiniformes | Opisthoproctidae | Winteria telescopa | native | Binocular fish | Japanese : Kuro-demenigisu |
| Stomiiformes | Phosichthyidae | Woodsia nonsuchae | native | Bigeye lightfish | Japanese : Tsumari-uki-eso |
| Tetraodontiformes | Balistidae | Xanthichthys auromarginatus | native | Gilded triggerfish | Japanese : Hoshimongara |
| Tetraodontiformes | Balistidae | Xanthichthys caeruleolineatus | native | Outrigger triggerfish | Japanese : Aosujimongara |
| Tetraodontiformes | Balistidae | Xanthichthys lineopunctatus | native | Striped triggerfish | Japanese : Suji namemongara |
| Tetraodontiformes | Balistidae | Xanthichthys mento | native | Redtail triggerfish | Japanese : Namemongara |
| Gobiiformes | Xenisthmidae | Xenisthmus clarus | native | Clear wriggler | Japanese : Yanagihaze |
| Gobiiformes | Xenisthmidae | Xenisthmus polyzonatus | native | Bullseye wriggler | Japanese : Mon-yanagihaze |
| Tetraodontiformes | Balistidae | Xenobalistes tumidipectoris | native | ||
| Perciformes/Uranoscopoidei | Uranoscopidae | Xenocephalus elongatus | native | Japanese : Aomishima | |
| Alepocephaliformes | Alepocephalidae | Xenodermichthys nodulosus | native | Japanese : Tsubu-iwashi | |
| Zeiformes | Grammicolepididae | Xenolepidichthys dalgleishi | native | Spotted tinselfish | Japanese : Hishi-matôdai |
| Perciformes/Zoarcoidei | Lumpenidae | Xenolumpenus longipterus | native | Japanese : Furisodegaji | |
| Blenniiformes | Blenniidae | Xiphasia matsubarai | native | Japanese snake blenny | Japanese : Hime-unagiginpo |
| Blenniiformes | Blenniidae | Xiphasia setifer | native | Hairtail blenny | Japanese : Unagiginpo |
| Carangiformes | Xiphiidae | Xiphias gladius | native | Swordfish | Japanese : Dakuda |
| Cyprinodontiformes | Poeciliidae | Xiphophorus hellerii | introduced | Green swordtail | |
| Cyprinodontiformes | Poeciliidae | Xiphophorus maculatus | introduced | Southern platyfish | |
| Ophidiiformes | Ophidiidae | Xyelacyba myersi | native | Gargoyle cusk | Japanese : Haridashi-ashiro |
| Anguilliformes | Ophichthidae | Xyrias revulsus | native | Strict snake eel | Japanese : Bô-umihebi |
| Kurtiformes | Apogonidae | Yarica hyalosoma | native | Humpbacked cardinalfish | Japanese : Kagami-tenjikudai |
| Anguilliformes | Ophichthidae | Yirrkala misolensis | native | Misol snake eel | |
| Gobiiformes | Gobiidae | Yongeichthys criniger | native | Japanese : Tsumugihaze | |
| Cypriniformes | Xenocyprididae | Zacco platypus | native | Freshwater minnow | Japanese : Oikawa |
| Squaliformes | Somniosidae | Zameus squamulosus | native | Velvet dogfish | Japanese : Birôdozame; Japanese : Suji-birôdozame; |
| Acanthuriformes | Zanclidae | Zanclus cornutus | native | Moorish idol | Japanese : Tsunodashi |
| Kurtiformes | Apogonidae | Zapogon evermanni | native | Evermann's cardinalfish | |
| Perciformes/Zoarcoidei | Zaproridae | Zaprora silenus | native | Prowfish | Japanese : Bôzuginpo |
| Acanthuriformes | Acanthuridae | Zebrasoma flavescens | native | Yellow tang | Japanese : Kiirohagi |
| Acanthuriformes | Acanthuridae | Zebrasoma scopas | native | Twotone tang | Japanese : Gomahagi |
| Acanthuriformes | Acanthuridae | Zebrasoma velifer | native | Sailfin tang | Japanese : Hirenagahagi |
| Pleuronectiformes | Soleidae | Zebrias japonica | native | Wavyband sole | Japanese : Seto-ushinoshita |
| Pleuronectiformes | Soleidae | Zebrias zebra | native | Zebra sole | Japanese : Shima-ushinoshita |
| Pleuronectiformes | Soleidae | Zebrias zebrinus | native | Japanese : Obi-ushinoshita | |
| Zeiformes | Zeniontidae | Zenion japonicum | native | Japanese dory | Japanese : Soko-matôdai |
| Zeiformes | Zeidae | Zenopsis nebulosa | native | Mirror dory | Japanese : Kagamidai |
| Perciformes/Cottoidei | Cottidae | Zesticelus bathybius | native | Japanese : Sokokajika | |
| Perciformes/Cottoidei | Cottidae | Zesticelus ochotensis | native | Japanese : Ohotsuku-soko-kajika | |
| Zeiformes | Zeidae | Zeus faber | native | John dory | Japanese : Matôdai |
| Perciformes/Zoarcoidei | Zoarcidae | Zoarces elongatus | native | Japanese : Nagagaji | |
| Perciformes/Zoarcoidei | Zoarcidae | Zoarces gillii | native | Japanese : Kôraigaji | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias glaber | native | Japanese : Tobi-itoginpo | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias hosoyai | native | Japanese : Noto kazunagi | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias macrocephalus | endemic | Japanese : Shinju kazunagi | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias major | native | Japanese : Ôkazunagi | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias neglectus | native | Japanese : Komon-itoginpo | |
| Perciformes/Zoarcoidei | Neozoarcidae | Zoarchias veneficus | native | Japanese : Kazunagi | |
| Kurtiformes | Apogonidae | Zoramia fragilis | native | Fragile cardinalfish | |
| Kurtiformes | Apogonidae | Zoramia gilberti | native | Gilbert's cardinalfish | Japanese : Usumomo-tenjikudai |
| Kurtiformes | Apogonidae | Zoramia leptacanthus | native | Threadfin cardinalfish | Japanese : Itohiki-tenjikudai |
| Kurtiformes | Apogonidae | Zoramia viridiventer | native | ||
| Lampriformes | Trachipteridae | Zu cristatus | native | Scalloped ribbonfish | Japanese : Yuki-furisode-uo |