Brachyhypopomus cunia is distinguished from other species of the genus Brachyhypopomus by the following combination of characters: 16-17 precaudal vertebrae (vs. 18-26 in B. alberti, B. arrayae, B. beebei, B. belindae, B. brevirostris, B. draco, B. flavipomus, B. gauderio, B. hamiltoni, B. janeiroensis, B. jureiae, B. palenque, B. pinnicaudatus, and B. verdii; head depth at eye 47.8-60.0% HL (vs. 36.3-47.7% in B. batesi, B. bombilla, B. provenzanoi, B. regani, and B. sullivani); presence of scales in middorsal region of anterior third of body (vs. absence in B. benjamini; pectoral fin with 10-13 rays (vs. 14-20 in B. bennetti, B. diazi, B. menezesi, and B. occidentalis); mouth width 24.8- 38.0% HL (vs. 15.7-22.6% in B. hendersoni). It has overlapping meristic counts and morphological measurements with B. bullocki and B. walteri, but can be diagnosed by having a very distinctive pigmentation pattern consisting of ventral portions of the flank, over the anal-fin pterygiophores, darkly pigmented, forming a dark stripe along the base of the anal fin (also shared with B. hendersoni), and numerous discrete dark spots (each has a cluster of dark chromatophores) which are scattered over the anal-fin pterygiophores, and in some specimens form an irregular dotted line along the lateral line (vs. absence of dark stripe along the anal-fin base and absence of discrete dark spots over the ventral flank in B. bullocki and B. walteri) (Ref. 116763).