A number of sources state that S. brandtii can be identified by the relatively anterior position of the anal-fin origin beneath the first few dorsal-fin rays. However, images of specimens collected from the rio São Francisco, where it is the only member of the genus present, suggest that this is not always the case and this is also supported by the figure from Eigenmann (1915). No recent diagnosis of the species is available.

Following Fink (1993), P. piraya can be distinguished from congeners by the following combination of characters: adipose fin with rays in larger specimens (vs. always without rays in other Pygocentrus species); branched dorsal-fin rays 15-18, usually 16 (vs. 14-18, usually 15); usually 7 neural spines anterior to first pterygiophore (vs. usually 6); vertebrae 36-39, usually 38 (vs. 35-38, usually 36). It can also be identified by colour pattern since it possesses distinctive bright yellow-orange pigmentation on the lower jaw, opercle and lateral body in life.