| Order | Family | Species | Occurrence | FishBase name | Name(s) in Territory |
|---|---|---|---|---|---|
| Siluriformes | Ariidae | Aceroichthys dioctes | native | Warrior catfish | |
| Gobiiformes | Eleotridae | Allomogurnda flavimarginata | native | ||
| Gobiiformes | Eleotridae | Allomogurnda hoesei | native | ||
| Gobiiformes | Eleotridae | Allomogurnda insularis | native | ||
| Gobiiformes | Eleotridae | Allomogurnda landfordorum | native | ||
| Gobiiformes | Eleotridae | Allomogurnda montana | native | ||
| Gobiiformes | Eleotridae | Allomogurnda multicincta | native | ||
| Gobiiformes | Eleotridae | Allomogurnda nesolepis | native | Yellowbelly gudgeon | |
| Gobiiformes | Eleotridae | Allomogurnda papua | native | ||
| Ovalentaria/misc | Ambassidae | Ambassis agrammus | native | Sailfin glass perchlet | English : Pale river perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis interrupta | native | Long-spined glass perchlet | English : Perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis macleayi | native | Macleay's glass perchlet | English : Macleay's perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis macracanthus | native | Estuarine glass perchlet | English : Estuarine perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis miops | native | Flag-tailed glass perchlet | English : Flag-tailed perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis nalua | native | Scalloped perchlet | English : Scalloped perchlet |
| Ovalentaria/misc | Ambassidae | Ambassis urotaenia | native | Banded-tail glassy perchlet | |
| Ovalentaria/misc | Ambassidae | Ambassis vachellii | native | Vachelli's glass perchlet | |
| Centrarchiformes | Terapontidae | Amniataba affinis | endemic | Tiger grunter | |
| Anabantiformes | Anabantidae | Anabas testudineus | introduced | Climbing perch | English : Climbing perch |
| Anguilliformes | Anguillidae | Anguilla bicolor | native | Indonesian shortfin eel | English : Indian short-finned eel |
| Anguilliformes | Anguillidae | Anguilla interioris | native | Highlands long-finned eel | English : New Guinea eel |
| Anguilliformes | Anguillidae | Anguilla marmorata | native | Giant mottled eel | English : Giant long-finned eel |
| Anguilliformes | Anguillidae | Anguilla megastoma | native | Polynesian longfinned eel | English : Pacific long-finned eel |
| Anguilliformes | Anguillidae | Anguilla obscura | native | Pacific shortfinned eel | English : Pacific short-finned eel |
| Anguilliformes | Anguillidae | Anguilla reinhardtii | native | Speckled longfin eel | |
| Beloniformes | Hemiramphidae | Arrhamphus sclerolepis | native | Northern snubnose garfish | English : Snub-nosed garfish |
| Gobiiformes | Gobiidae | Awaous acritosus | native | Roman nose goby | |
| Gobiiformes | Gobiidae | Awaous guamensis | native | ||
| Gobiiformes | Gobiidae | Awaous melanocephalus | native | Largesnout goby | |
| Gobiiformes | Eleotridae | Belobranchus belobranchus | native | Throat-spine gudgeon | English : Throat-spine gudgeon |
| Siluriformes | Ariidae | Bleekeriella leptaspis | native | Salmon catfish | English : Triangular-shield catfish |
| Gobiiformes | Oxudercidae | Boleophthalmus boddarti | native | Boddart's goggle-eyed goby | English : Boddart's goggle-eyed goby |
| Gobiiformes | Butidae | Bostrychus strigogenys | native | Striped-cheek gudgeon | English : Striped-cheek gudgeon |
| Gobiiformes | Butidae | Bostrychus zonatus | native | Barred gudgeon | |
| Pleuronectiformes | Soleidae | Brachirus villosus | native | Velvety sole | English : Velvety sole |
| Gobiiformes | Gobiidae | Brachyamblyopus brachysoma | native | ||
| Siluriformes | Ariidae | Brustiarius nox | endemic | Comb-gilled catfish | English : Comb-gilled catfish |
| Siluriformes | Ariidae | Brustiarius solidus | native | Hard-palate catfish | English : Hard-plate catfish |
| Siluriformes | Ariidae | Brustiarius utarus | native | Northern rivers catfish | |
| Gobiiformes | Eleotridae | Bunaka gyrinoides | native | Greenback gauvina | English : Green-backed gauvina |
| Gobiiformes | Butidae | Butis amboinensis | native | Olive flathead-gudgeon | English : Olive flathead-gudgeon |
| Gobiiformes | Butidae | Butis butis | native | Duckbill sleeper | English : Crimson-tipped gudgeon |
| Gobiiformes | Butidae | Butis melanostigma | native | Black-spotted gudgeon | |
| Gobiiformes | Gobiidae | Caragobius urolepis | native | Scaleless worm goby | |
| Carangiformes | Carangidae | Caranx sexfasciatus | native | Bigeye trevally | English : Bigeye trevally |
| Carcharhiniformes | Carcharhinidae | Carcharhinus leucas | native | Bull shark | English : Bull shark |
| Mugiliformes | Mugilidae | Cestraeus goldiei | native | Goldie river mullet | |
| Mugiliformes | Mugilidae | Cestraeus plicatilis | native | Lobed river mullet | English : Goldie river mullet |
| Anabantiformes | Channidae | Channa striata | introduced | Striped snakehead | |
| Gonorynchiformes | Chanidae | Chanos chanos | native | Milkfish | |
| Atheriniformes | Melanotaeniidae | Chilatherina axelrodi | endemic | Axelrod's rainbowfish | English : Axelrod's rainbowfish |
| Atheriniformes | Melanotaeniidae | Chilatherina bulolo | endemic | Bulolo rainbowfish | |
| Atheriniformes | Melanotaeniidae | Chilatherina campsi | endemic | Highlands rainbowfish | English : Highlands rainbowfish |
| Atheriniformes | Melanotaeniidae | Chilatherina crassispinosa | native | Silver rainbowfish | English : Stiff-rayed rainbowfish |
| Atheriniformes | Melanotaeniidae | Chilatherina fasciata | native | Barred rainbowfish | English : Barred rainbowfish |
| Atheriniformes | Melanotaeniidae | Chilatherina lorentzii | native | Lorentz's rainbowfish | English : Lorentz' rainbowfish |
| Atheriniformes | Melanotaeniidae | Chilatherina pagwiensis | native | ||
| Siluriformes | Ariidae | Cinetodus froggatti | native | Smallmouthed salmon catfish | English : Frogatt's catfish |
| Siluriformes | Clariidae | Clarias batrachus | introduced | Philippine catfish | |
| Clupeiformes | Ehiravidae | Clupeoides papuensis | native | Papuan river sprat | English : Toothed river-herring |
| Clupeiformes | Ehiravidae | Clupeoides venulosus | native | West Irian river sprat | English : River sprat |
| Siluriformes | Ariidae | Cochlefelis danielsi | native | Daniel's catfish | English : Daniel's catfish |
| Siluriformes | Ariidae | Cochlefelis insidiator | native | Flat catfish | |
| Siluriformes | Ariidae | Cochlefelis spatula | native | Duckbilled catfish | English : Duck-billed catfish |
| Cichliformes | Cichlidae | Coptodon rendalli | introduced | Redbreast tilapia | |
| Atheriniformes | Atherinidae | Craterocephalus kailolae | endemic | Kailola's hardyhead | |
| Atheriniformes | Atherinidae | Craterocephalus lacustris | endemic | Kutubu hardyhead | English : Kutubu hardyhead |
| Atheriniformes | Atherinidae | Craterocephalus nouhuysi | native | Mountain hardyhead | |
| Atheriniformes | Atherinidae | Craterocephalus pimatuae | endemic | Pima hardyhead | English : Pima hardyhead |
| Atheriniformes | Atherinidae | Craterocephalus randi | native | Kubuna hardyhead | English : Kubuna River hardyhead |
| Pleuronectiformes | Cynoglossidae | Cynoglossus heterolepis | native | Freshwater tongue sole | |
| Cypriniformes | Cyprinidae | Cyprinus carpio | introduced | Common carp | |
| Acanthuriformes | Lobotidae | Datnioides campbelli | native | ||
| Acanthuriformes | Lobotidae | Datnioides polota | native | English : Four-banded triple-tail | |
| Ovalentaria/misc | Ambassidae | Denariusa australis | native | Pennyfish | |
| Tetraodontiformes | Tetraodontidae | Dichotomyctere erythrotaenia | native | Red-striped toadfish | |
| Siluriformes | Ariidae | Doiichthys novaeguineae | native | Spoon-snouted catfish | English : Spoon-snouted catfish |
| Gobiiformes | Gobiidae | Drombus globiceps | native | Kranji drombus | |
| Gobiiformes | Eleotridae | Eleotris aquadulcis | endemic | Freshwater gudgeon | |
| Gobiiformes | Eleotridae | Eleotris fusca | native | Dusky sleeper | English : Brown gudgeon |
| Gobiiformes | Eleotridae | Eleotris melanosoma | native | Broadhead sleeper | English : Black gudgeon |
| Perciformes/Serranoidei | Epinephelidae | Epinephelus polystigma | native | White-dotted grouper | |
| Clupeiformes | Dorosomatidae | Escualosa thoracata | native | White sardine | English : Deep-bodied herring |
| Kurtiformes | Apogonidae | Fibramia amboinensis | native | Amboina cardinalfish | English : Amboina cardinalfish |
| Cyprinodontiformes | Poeciliidae | Gambusia affinis | introduced | Mosquitofish | English : Mosquitofish |
| Eupercaria/misc | Gerreidae | Gerres filamentosus | native | Whipfin silverbiddy | English : Threadfin silver-biddy |
| Gobiiformes | Eleotridae | Giuris margaritaceus | native | Snakehead gudgeon | English : Snake-headed gudgeon |
| Kurtiformes | Apogonidae | Glossamia abo | native | ||
| Kurtiformes | Apogonidae | Glossamia aprion | native | Mouth almighty | English : Mouth almighty |
| Kurtiformes | Apogonidae | Glossamia gjellerupi | native | Gjellerup's mouth almighty | English : Gjellerup's cardinalfish |
| Kurtiformes | Apogonidae | Glossamia narindica | endemic | Slender mouth almighty | English : Slender mouth almighty |
| Kurtiformes | Apogonidae | Glossamia sandei | native | Sande's mouth almighty | |
| Kurtiformes | Apogonidae | Glossamia trifasciata | native | Three-barred mouth almighty | |
| Kurtiformes | Apogonidae | Glossamia wichmanni | native | Wichmann's mouth almighty | English : Wichmann's cardinalfish |
| Gobiiformes | Gobiidae | Glossogobius aureus | native | Golden tank goby | |
| Gobiiformes | Gobiidae | Glossogobius bicirrhosus | native | Bearded flathead goby | |
| Gobiiformes | Gobiidae | Glossogobius brunnoides | native | Dusky mountain goby | English : Dusky mountain goby |
| Gobiiformes | Gobiidae | Glossogobius bulmeri | native | Bulmer's goby | English : Bulmer's goby |
| Gobiiformes | Gobiidae | Glossogobius celebius | native | Celebes goby | |
| Gobiiformes | Gobiidae | Glossogobius circumspectus | native | Circumspect goby | |
| Gobiiformes | Gobiidae | Glossogobius clitellus | native | ||
| Gobiiformes | Gobiidae | Glossogobius coatesi | endemic | Coates' goby | |
| Gobiiformes | Gobiidae | Glossogobius concavifrons | native | Concave goby | |
| Gobiiformes | Gobiidae | Glossogobius giuris | native | Tank goby | English : Flat-headed goby |
| Gobiiformes | Gobiidae | Glossogobius koragensis | native | Koragu tank goby | |
| Gobiiformes | Gobiidae | Glossogobius macrocephalus | endemic | ||
| Gobiiformes | Gobiidae | Glossogobius multipapillus | endemic | ||
| Gobiiformes | Gobiidae | Glossogobius munroi | native | ||
| Gobiiformes | Gobiidae | Glossogobius muscorum | native | ||
| Gobiiformes | Gobiidae | Glossogobius nanus | native | ||
| Gobiiformes | Gobiidae | Glossogobius pumilus | native | ||
| Gobiiformes | Gobiidae | Glossogobius robertsi | native | ||
| Gobiiformes | Gobiidae | Glossogobius sentaniensis | endemic | ||
| Gobiiformes | Gobiidae | Glossogobius torrentis | endemic | White water goby | |
| Atheriniformes | Melanotaeniidae | Glossolepis kabia | native | ||
| Atheriniformes | Melanotaeniidae | Glossolepis maculosa | endemic | Spotted rainbowfish | English : Spotted rainbowfish |
| Atheriniformes | Melanotaeniidae | Glossolepis multisquamata | native | Sepik rainbowfish | English : Rosy rainbowfish |
| Atheriniformes | Melanotaeniidae | Glossolepis ramuensis | endemic | Ramu rainbowfish | English : Ramu rainbowfish |
| Atheriniformes | Melanotaeniidae | Glossolepis wanamensis | endemic | Lake Wanam rainbowfish | English : Lake Wanam rainbowfish |
| Carcharhiniformes | Carcharhinidae | Glyphis glyphis | native | Speartooth shark | English : Speartooth shark |
| Gobiiformes | Gobiidae | Gobiopterus semivestitus | native | Glassgoby | |
| Gobiiformes | Gobiidae | Gymnoamblyopus novaeguineae | native | ||
| Anguilliformes | Muraenidae | Gymnothorax polyuranodon | native | Freshwater moray | English : Freshwater moray |
| Gobiiformes | Gobiidae | Hemigobius hoevenii | native | Banded mulletgoby | |
| Centrarchiformes | Terapontidae | Hephaestus adamsoni | endemic | Adamson's grunter | English : Adamson's grunter |
| Centrarchiformes | Terapontidae | Hephaestus habbemai | native | Mountain grunter | |
| Centrarchiformes | Terapontidae | Hephaestus komaensis | native | ||
| Centrarchiformes | Terapontidae | Hephaestus obtusifrons | native | English : Striped grunter | |
| Centrarchiformes | Terapontidae | Hephaestus raymondi | endemic | Raymond's grunter | English : Ray Moore's grunter |
| Centrarchiformes | Terapontidae | Hephaestus transmontanus | endemic | Sepik grunter | English : Northern grunter |
| Centrarchiformes | Terapontidae | Hephaestus trimaculatus | endemic | Threespot grunter | English : Threespot grunter |
| Clupeiformes | Dorosomatidae | Herklotsichthys castelnaui | native | Castelnau's herring | |
| Syngnathiformes | Syngnathidae | Hippichthys heptagonus | native | Belly pipefish | English : Reticulated freshwater pipefish |
| Syngnathiformes | Syngnathidae | Hippichthys penicillus | native | Beady pipefish | English : Steep-nosed pipefish |
| Gobiiformes | Eleotridae | Hypseleotris compressa | native | Empire gudgeon | English : Australian carp-gudgeon |
| Gobiiformes | Eleotridae | Hypseleotris cyprinoides | native | Tropical carp-gudgeon | English : Tropical carp-gudgeon |
| Gobiiformes | Eleotridae | Hypseleotris guentheri | native | ||
| Atheriniformes | Melanotaeniidae | Iriatherina werneri | native | Threadfin rainbowfish | |
| Eupercaria/misc | Sciaenidae | Johnius australis | native | Bottlenose jewfish | |
| Atheriniformes | Pseudomugilidae | Kiunga ballochi | endemic | Glass blue-eye | English : Glass blue-eye |
| Atheriniformes | Pseudomugilidae | Kiunga bleheri | native | ||
| Centrarchiformes | Kuhliidae | Kuhlia marginata | native | Dark-margined flagtail | English : Spotted flagtail |
| Centrarchiformes | Kuhliidae | Kuhlia rupestris | native | Rock flagtail | English : Rock flagtail |
| Kurtiformes | Kurtidae | Kurtus gulliveri | native | Nurseryfish | English : Nurseryfish |
| Anguilliformes | Ophichthidae | Lamnostoma kampeni | native | Freshwater snake-eel | |
| Anguilliformes | Ophichthidae | Lamnostoma mindora | native | ||
| Carangaria/misc | Latidae | Lates calcarifer | native | Barramundi | English : Barramundi |
| Acanthuriformes | Leiognathidae | Leiognathus equula | native | Common ponyfish | English : Common ponyfish |
| Gobiiformes | Gobiidae | Lentipes multiradiatus | native | ||
| Gobiiformes | Gobiidae | Lentipes venustus | native | ||
| Gobiiformes | Gobiidae | Lentipes watsoni | native | ||
| Pleuronectiformes | Soleidae | Leptachirus bensbach | native | Bensbach River Sole | |
| Pleuronectiformes | Soleidae | Leptachirus kikori | native | Kikori River Sole | |
| Pleuronectiformes | Soleidae | Leptachirus robertsi | native | Robert's Sole | |
| Syngnathiformes | Syngnathidae | Lophocampus brevidorsalis | native | Stream pipefish | |
| Eupercaria/misc | Lutjanidae | Lutjanus argentimaculatus | native | Mangrove red snapper | English : Mangrove jack |
| Eupercaria/misc | Lutjanidae | Lutjanus fuscescens | native | Freshwater snapper | English : Dusky snapper |
| Eupercaria/misc | Lutjanidae | Lutjanus goldiei | endemic | Papuan black snapper | English : Papuan black bass |
| Eupercaria/misc | Lutjanidae | Lutjanus maxweberi | native | Pygmy snapper | English : Pygmy snapper |
| Tetraodontiformes | Tetraodontidae | Marilyna pleurosticta | native | ||
| Elopiformes | Megalopidae | Megalops cyprinoides | native | Indo-Pacific tarpon | English : Ox-eye herring |
| Siluriformes | Ariidae | Megalosciades augustus | endemic | Short barbelled catfish | English : Short-barbelled catfish |
| Blenniiformes | Blenniidae | Meiacanthus anema | native | Threadless blenny | English : Threadless blenny |
| Atheriniformes | Melanotaeniidae | Melanotaenia affinis | native | North New Guinea rainbowfish | English : Red-finned rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia caerulea | native | Blue rainbowfish | English : Blue rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia goldiei | native | Goldie River rainbowfish | English : Gold-line rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia herbertaxelrodi | endemic | Lake Tebera rainbowfish | English : Lake Tebera rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia iris | endemic | Strickland rainbowfish | English : Strickland rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia lacustris | endemic | Lake Kutubu rainbowfish | English : Lake Kutubu rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia monticola | endemic | Mountain rainbowfish | English : Mountain rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia mubiensis | native | Mubi rainbowfish | English : Mubi rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia oktediensis | endemic | Oktedi rainbowfish | English : Oktedi rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia papuae | endemic | Papuan rainbowfish | English : Papua rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia parkinsoni | endemic | Parkinson's rainbowfish | English : Parkinson's rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia pimaensis | endemic | Pima River rainbowfish | |
| Atheriniformes | Melanotaeniidae | Melanotaenia rubrostriata | native | Red-striped rainbowfish | English : Red-striped rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia sahulensis | native | Sahul rainbowfish | |
| Atheriniformes | Melanotaeniidae | Melanotaenia sexlineata | endemic | Fly River rainbowfish | English : Fly River rainbowfish |
| Atheriniformes | Melanotaeniidae | Melanotaenia sylvatica | native | ||
| Centrarchiformes | Terapontidae | Mesopristes argenteus | native | Silver grunter | English : Silver grunter |
| Centrarchiformes | Terapontidae | Mesopristes cancellatus | native | Tapiroid grunter | English : Tapiroid grunter |
| Centrarchiformes | Terapontidae | Mesopristes iravi | native | ||
| Syngnathiformes | Syngnathidae | Microphis brachyurus | native | Short-tailed pipefish | English : Short-tailed pipefish |
| Syngnathiformes | Syngnathidae | Microphis leiaspis | native | Barhead pipefish | |
| Syngnathiformes | Syngnathidae | Microphis manadensis | native | Menado pipefish | English : Menado pipefish |
| Syngnathiformes | Syngnathidae | Microphis mento | native | ||
| Syngnathiformes | Syngnathidae | Microphis millepunctatus | native | Shorttail pipefish | |
| Syngnathiformes | Syngnathidae | Microphis nicoleae | native | ||
| Syngnathiformes | Syngnathidae | Microphis spinachioides | native | Spinach pipefish | English : Spinach pipefish |
| Gobiiformes | Eleotridae | Mogurnda aurifodinae | native | Northern mogurnda | |
| Gobiiformes | Eleotridae | Mogurnda cingulata | native | Banded mogurnda | |
| Gobiiformes | Eleotridae | Mogurnda furva | endemic | Black mogurnda | English : Black mogurnda |
| Gobiiformes | Eleotridae | Mogurnda kutubuensis | endemic | Lake Kutubu mogurnda | |
| Gobiiformes | Eleotridae | Mogurnda lineata | endemic | Kokoda mogurnda | English : Kokoda mogurnda |
| Gobiiformes | Eleotridae | Mogurnda maccuneae | endemic | ||
| Gobiiformes | Eleotridae | Mogurnda malsmithi | native | ||
| Gobiiformes | Eleotridae | Mogurnda mogurnda | native | Northern trout gudgeon | English : Purple-spotted gudgeon |
| Gobiiformes | Eleotridae | Mogurnda mosa | endemic | ||
| Gobiiformes | Eleotridae | Mogurnda orientalis | endemic | Eastern mogurnda | English : Eastern mogurnda |
| Gobiiformes | Eleotridae | Mogurnda pulchra | endemic | Moresby mogurnda | |
| Gobiiformes | Eleotridae | Mogurnda spilota | endemic | Blotched mogurnda | English : Blotched mogurnda |
| Gobiiformes | Eleotridae | Mogurnda variegata | endemic | Variegated mogurnda | English : Variegated mogurnda |
| Gobiiformes | Eleotridae | Mogurnda vitta | endemic | Striped mogurnda | English : Striped mogurnda |
| Eupercaria/misc | Monodactylidae | Monodactylus argenteus | native | Silver moony | English : Silver moonfish |
| Mugiliformes | Mugilidae | Moolgarda buchanani | native | Bluetail mullet | English : Blue-tail mullet |
| Mugiliformes | Mugilidae | Moolgarda heterocheilos | native | Half fringelip mullet | English : Fringe-lipped mullet |
| Mugiliformes | Mugilidae | Mugil cephalus | native | Flathead grey mullet | English : Sea mullet |
| Gobiiformes | Gobiidae | Mugilogobius filifer | native | Threadfin mangrovegoby | |
| Gobiiformes | Gobiidae | Mugilogobius fusculus | native | Obscure goby | English : One-thread goby |
| Gobiiformes | Gobiidae | Mugilogobius mertoni | native | Chequered mangrove goby | |
| Gobiiformes | Gobiidae | Mugilogobius notospilus | native | Freshwater mangrovegoby | |
| Gobiiformes | Gobiidae | Mugilogobius rambaiae | native | Queen of Siam goby | |
| Siluriformes | Ariidae | Nedystoma dayi | native | Day's catfish | English : Day's catfish |
| Clupeiformes | Dorosomatidae | Nematalosa erebi | native | Australian river gizzard shad | English : Australian river gizzard shad |
| Clupeiformes | Dorosomatidae | Nematalosa flyensis | endemic | Fly river gizzard shad | English : Fly river gizzard shad |
| Clupeiformes | Dorosomatidae | Nematalosa papuensis | endemic | Strickland river gizzard shad | English : Strickland River herring |
| Siluriformes | Ariidae | Neoarius berneyi | native | Highfin catfish | English : Berney's catfish |
| Siluriformes | Ariidae | Neoarius graeffei | native | Blue salmon catfish | English : Salmon catfish |
| Siluriformes | Plotosidae | Neosilurus ater | native | Narrowfront tandan | English : Narrow-fronted tandan |
| Siluriformes | Plotosidae | Neosilurus brevidorsalis | native | Shortfin tandan | English : Short-finned tandan |
| Siluriformes | Plotosidae | Neosilurus coatesi | native | ||
| Siluriformes | Plotosidae | Neosilurus equinus | native | Southern tandan | English : Gjellerup's tandan |
| Siluriformes | Plotosidae | Neosilurus gjellerupi | native | Northern tandan | English : Coates' tandan |
| Siluriformes | Plotosidae | Neosilurus idenburgi | native | Idenburg tandan | English : Idenburg River tandan |
| Siluriformes | Plotosidae | Neosilurus novaeguineae | native | New Guinea tandan | |
| Eupercaria/misc | Sciaenidae | Nibea soldado | native | Soldier croaker | |
| Eupercaria/misc | Sciaenidae | Nibea squamosa | native | Scale croaker | |
| Gobiiformes | Gobiidae | Oligolepis acutipennis | native | Sharptail goby | |
| Gobiiformes | Gobiidae | Oligolepis stomias | native | ||
| Siluriformes | Plotosidae | Oloplotosus luteus | endemic | Pale yellow tandan | English : Pale yellow tandan |
| Siluriformes | Plotosidae | Oloplotosus mariae | native | Maria's tandan | |
| Siluriformes | Plotosidae | Oloplotosus torobo | endemic | Kutubu tandan | English : Kutubu tandan |
| Blenniiformes | Blenniidae | Omobranchus ferox | native | Gossamer blenny | English : Gossamer blenny |
| Salmoniformes | Salmonidae | Oncorhynchus mykiss | introduced | Rainbow trout | English : Rainbow trout |
| Gobiiformes | Butidae | Ophiocara gigas | native | Giant mud-gudgeon | |
| Synbranchiformes | Synbranchidae | Ophisternon bengalense | native | Bengal eel | English : One-gilled eel |
| Synbranchiformes | Synbranchidae | Ophisternon gutturale | native | Australian swamp eel | |
| Cichliformes | Cichlidae | Oreochromis mossambicus | introduced | Mozambique tilapia | English : Tilapia |
| Anabantiformes | Osphronemidae | Osphronemus goramy | introduced | Giant gourami | English : Giant gouramy |
| Gobiiformes | Oxudercidae | Oxuderces wirzi | native | Wirz's goby | English : Wirz's goby |
| Gobiiformes | Butidae | Oxyeleotris aruensis | native | Aru gudgeon | English : Aru Island gudgeon |
| Gobiiformes | Butidae | Oxyeleotris caeca | endemic | ||
| Gobiiformes | Butidae | Oxyeleotris fimbriata | native | Fimbriate gudgeon | English : Rough-scaled loter |
| Gobiiformes | Butidae | Oxyeleotris herwerdenii | native | Blackbanded gauvina | English : Black-banded gauvina |
| Gobiiformes | Butidae | Oxyeleotris heterodon | native | Sentani gudgeon | |
| Gobiiformes | Butidae | Oxyeleotris lineolata | native | Sleepy cod | English : Black-banded loter |
| Gobiiformes | Butidae | Oxyeleotris nullipora | native | Poreless gudgeon | |
| Gobiiformes | Butidae | Oxyeleotris paucipora | native | Fewpored gudgeon | |
| Gobiiformes | Butidae | Oxyeleotris urophthalmus | native | ||
| Siluriformes | Ariidae | Pachyula crassilabris | endemic | Thick-lipped catfish | English : Thick-lipped catfish |
| Siluriformes | Ariidae | Papuarius latirostris | native | Broad-snouted catfish | English : Broad-snouted catfish |
| Siluriformes | Ariidae | Paracinetodus carinatus | native | Comb-spined catfish | English : Comb-spined catfish |
| Ovalentaria/misc | Ambassidae | Parambassis confinis | native | Sepik glass perchlet | English : Sepik River perchlet |
| Ovalentaria/misc | Ambassidae | Parambassis gulliveri | native | Giant glassfish | English : Giant river perchlet |
| Mugiliformes | Mugilidae | Paramugil parmatus | native | Broad-mouthed mullet | |
| Pleuronectiformes | Soleidae | Pardachirus poropterus | native | Estuary sole | |
| Pleuronectiformes | Soleidae | Pardachirus rautheri | native | ||
| Gobiiformes | Oxudercidae | Periophthalmus argentilineatus | native | Barred mudskipper | English : Barred mudskipper |
| Characiformes | Serrasalmidae | Piaractus brachypomus | introduced | Pirapitinga | |
| Centrarchiformes | Terapontidae | Pingalla lorentzi | native | Lorentz's grunter | English : Lorentz's grunter |
| Mugiliformes | Mugilidae | Planiliza alata | native | Diamond mullet | English : Basket mullet |
| Mugiliformes | Mugilidae | Planiliza macrolepis | native | Largescale mullet | English : Large-scaled mullet |
| Mugiliformes | Mugilidae | Planiliza melinoptera | native | Otomebora mullet | English : Cream mullet |
| Mugiliformes | Mugilidae | Planiliza ordensis | native | River Diamond mullet | |
| Mugiliformes | Mugilidae | Planiliza planiceps | native | Tade gray mullet | English : Rock mullet |
| Mugiliformes | Mugilidae | Planiliza subviridis | native | Greenback mullet | English : Green back mullet |
| Siluriformes | Ariidae | Plicofollis polystaphylodon | native | Mozambique sea catfish | |
| Siluriformes | Plotosidae | Plotosus papuensis | native | Papuan eel-catfish | English : Papuan catfish-eel |
| Cyprinodontiformes | Poeciliidae | Poecilia reticulata | introduced | Guppy | English : Guppy |
| Carangaria/misc | Polynemidae | Polydactylus macrochir | native | King threadfin | English : Longfinned threadfin |
| Siluriformes | Plotosidae | Porochilus meraukensis | native | Merauke tandan | English : Merauke River catfish |
| Siluriformes | Plotosidae | Porochilus obbesi | native | Obbes' catfish | English : Obbes' catfish |
| Siluriformes | Ariidae | Potamosilurus coatesi | endemic | Coates' catfish | |
| Siluriformes | Ariidae | Potamosilurus macrorhynchus | native | Sharp-nosed catfish | English : Sharp-nosed catfish |
| Siluriformes | Ariidae | Potamosilurus taylori | native | Taylor's catfish | English : Taylor's catfish |
| Siluriformes | Ariidae | Potamosilurus velutinus | native | Papillate catfish | English : Papillate catfish |
| Gobiiformes | Butidae | Prionobutis microps | native | Small-eyed loter | English : Small-eyed loter |
| Rhinopristiformes | Pristidae | Pristis microdon | native | Largetooth sawfish | English : Sawfish |
| Gobiiformes | Gobiidae | Pseudogobiopsis rubrimaculosa | native | ||
| Gobiiformes | Gobiidae | Pseudogobius melanosticta | native | Black-spotted snubnose goby | |
| Gobiiformes | Gobiidae | Pseudogobius poicilosoma | native | Northern fatnose goby | |
| Atheriniformes | Pseudomugilidae | Pseudomugil connieae | endemic | Popondetta blue-eye | English : Popondetta blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil furcatus | endemic | Forktail rainbowfish | English : Forktail blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil gertrudae | native | Spotted blue-eye | English : Gertrude's blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil inconspicuus | native | Inconspicuous blue-eye | English : Tiny blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil novaeguineae | native | New Guinea blue-eye | English : New Guinea blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil paludicola | native | Swamp blue-eye | |
| Atheriniformes | Pseudomugilidae | Pseudomugil paskai | endemic | Paska's blue-eye | English : Paska's blue-eye |
| Atheriniformes | Pseudomugilidae | Pseudomugil tenellus | native | Delicate blue-eye | |
| Gobiiformes | Gobiidae | Redigobius balteatus | native | Rhinohorn goby | |
| Gobiiformes | Gobiidae | Redigobius bikolanus | native | Speckled goby | |
| Gobiiformes | Gobiidae | Redigobius chrysosoma | native | ||
| Gobiiformes | Gobiidae | Redigobius nanus | native | ||
| Gobiiformes | Gobiidae | Redigobius oyensi | native | ||
| Gobiiformes | Gobiidae | Redigobius tambujon | native | ||
| Gobiiformes | Rhyacichthyidae | Rhyacichthys aspro | native | Loach goby | English : Loach goby |
| Salmoniformes | Salmonidae | Salmo trutta | introduced | Sea trout | English : Brown trout |
| Salmoniformes | Salmonidae | Salvelinus fontinalis | introduced | Brook trout | English : Brook trout |
| Acanthuriformes | Scatophagidae | Scatophagus argus | native | Spotted scat | English : Spotted scat |
| Gobiiformes | Gobiidae | Schismatogobius alleni | native | ||
| Gobiiformes | Gobiidae | Schismatogobius baitabag | native | ||
| Gobiiformes | Gobiidae | Schismatogobius bruynisi | native | ||
| Osteoglossiformes | Osteoglossidae | Scleropages jardinii | native | Australian bonytongue | English : Jardine's barramundi |
| Clupeiformes | Engraulidae | Setipinna tenuifilis | native | Common hairfin anchovy | English : Hairfin anchovy |
| Gobiiformes | Gobiidae | Sicyopterus cynocephalus | native | Cleft-lipped goby | |
| Gobiiformes | Gobiidae | Sicyopterus lengguru | native | ||
| Gobiiformes | Gobiidae | Sicyopterus longifilis | native | Threadfin goby | |
| Gobiiformes | Gobiidae | Sicyopterus micrurus | native | Clinging goby | |
| Gobiiformes | Gobiidae | Sicyopterus ocellaris | native | ||
| Gobiiformes | Gobiidae | Sicyopterus stiphodonoides | native | ||
| Gobiiformes | Gobiidae | Sicyopus beremeensis | native | ||
| Gobiiformes | Gobiidae | Sicyopus discordipinnis | native | ||
| Gobiiformes | Gobiidae | Sicyopus zosterophorus | native | ||
| Eupercaria/misc | Sillaginidae | Sillago sihama | native | Silver sillago | English : Northern whiting |
| Mugiliformes | Mugilidae | Squalomugil nasutus | native | Shark mullet | English : Mud mullet |
| Gobiiformes | Gobiidae | Stenogobius alleni | native | ||
| Gobiiformes | Gobiidae | Stenogobius beauforti | native | Beaufort's goby | |
| Gobiiformes | Gobiidae | Stenogobius genivittatus | native | Chinstripe goby | English : Chin-band goby |
| Gobiiformes | Gobiidae | Stenogobius hoesei | native | ||
| Gobiiformes | Gobiidae | Stenogobius laterisquamatus | native | ||
| Gobiiformes | Gobiidae | Stenogobius psilosinionus | native | ||
| Gobiiformes | Gobiidae | Stenogobius watsoni | native | ||
| Gobiiformes | Gobiidae | Stiphodon atratus | native | Black stiphodon | |
| Gobiiformes | Gobiidae | Stiphodon birdsong | native | ||
| Gobiiformes | Gobiidae | Stiphodon elegans | native | ||
| Gobiiformes | Gobiidae | Stiphodon larson | native | ||
| Gobiiformes | Gobiidae | Stiphodon rutilaureus | native | Golden-red stiphodon | |
| Gobiiformes | Gobiidae | Stiphodon semoni | native | ||
| Clupeiformes | Engraulidae | Stolephorus indicus | native | Indian anchovy | English : Indian anchovy |
| Clupeiformes | Engraulidae | Stolephorus waitei | native | Spotty-face anchovy | |
| Beloniformes | Belonidae | Strongylura krefftii | native | Long tom | English : Freshwater long-tom |
| Beloniformes | Belonidae | Strongylura strongylura | native | Spottail needlefish | English : Spottail needlefish |
| Kurtiformes | Apogonidae | Taeniamia buruensis | native | Buru cardinalfish | English : Buru cardinalfish |
| Gobiiformes | Gobiidae | Taenioides anguillaris | native | Eel worm goby | |
| Gobiiformes | Gobiidae | Taenioides cirratus | native | Bearded worm goby | |
| Gobiiformes | Eleotridae | Tateurndina ocellicauda | endemic | Peacock gudgeon | English : Peacock-eye gudgeon |
| Centrarchiformes | Terapontidae | Terapon jarbua | native | Jarbua terapon | English : Crescent perch |
| Ovalentaria/misc | Ambassidae | Tetracentrum apogonoides | endemic | Four-spined glass perchlet | English : Four-spined perchlet |
| Ovalentaria/misc | Ambassidae | Tetracentrum caudovittatus | endemic | Kokoda glass perchlet | |
| Ovalentaria/misc | Ambassidae | Tetracentrum honessi | endemic | Honess' glass perchlet | English : Honess' perchlet |
| Clupeiformes | Engraulidae | Thryssa rastrosa | endemic | Fly river thryssa | |
| Clupeiformes | Engraulidae | Thryssa scratchleyi | native | New Guinea thryssa | English : Freshwater anchovy |
| Carangaria/misc | Toxotidae | Toxotes chatareus | native | Spotted archerfish | |
| Carangaria/misc | Toxotidae | Toxotes jaculatrix | native | Banded archerfish | |
| Carangaria/misc | Toxotidae | Toxotes lorentzi | native | Primitive archerfish | |
| Anabantiformes | Osphronemidae | Trichopodus pectoralis | introduced | Snakeskin gourami | English : Snakeskin gouramy |
| Anabantiformes | Osphronemidae | Trichopodus trichopterus | introduced | Three spot gourami | English : Three-spot gouramy |
| Myliobatiformes | Dasyatidae | Urogymnus polylepis | native | Giant freshwater whipray | |
| Centrarchiformes | Terapontidae | Variichthys lacustris | endemic | Lake grunter | English : Lake grunter |
| Cyprinodontiformes | Poeciliidae | Xiphophorus hellerii | introduced | Green swordtail | English : Swordtail |
| Kurtiformes | Apogonidae | Yarica hyalosoma | native | Humpbacked cardinalfish | English : Humpbacked cardinalfish |
| Gobiiformes | Oxudercidae | Zappa confluentus | native | Slender mudskipper | |
| Beloniformes | Zenarchopteridae | Zenarchopterus caudovittatus | native | Long-jawed river garfish | English : Long-jawed river-garfish |
| Beloniformes | Zenarchopteridae | Zenarchopterus dispar | native | Feathered river-garfish | English : Feathered river-garfish |
| Beloniformes | Zenarchopteridae | Zenarchopterus kampeni | native | Sepik River halfbeak | English : Sepik River halfbeak |
| Beloniformes | Zenarchopteridae | Zenarchopterus novaeguineae | native | Fly River garfish | English : Fly river-garfish |
| Beloniformes | Zenarchopteridae | Zenarchopterus quadrimaculatus | native | ||
| Beloniformes | Zenarchopteridae | Zenarchopterus robertsi | endemic | Robert's river garfish | English : Robert's river-garfish |