Brachyhypopomus hendersoni is distinguished from other species of the genus Brachyhypopomus by the following combination of characters: caudal filament length 32.3-64.5% length to end of anal fin (vs. 7.4-31.6% in B. alberti, B. arrayae, B. batesi, B. belindae, B. benjamini, B. bennetti, B. bombilla, B. hamiltoni, B. occidentalis, B. palenque, B. provenzanoi, B. regani, B. sullivani, and B. verdii); 15-17 precaudal vertebrae (vs. 18-25 in B. beebei, B. brevirostris, B. draco, B. flavipomus, B. gauderio, B. janeiroensis, B. jureiae, and B. pinnicaudatus); head width at occiput 39.2-47.8% HL (vs. 49.5-70.4% in B. bullocki, B. diazi, and B. menezesi); and dorsal rami of the recurrent branch of the anterior lateral line nerve not visible (vs. visible in B. cunia and B. walteri) (Ref. 116763).