This species is distinguished from most congeners, except H. mikrostiktos, H. paez, H. tridens, and H. virolinica, by the number of branched anal-fin rays 15-19 (vs. 20-34); Hemibrycon beni differs from these species by the number of lateral line scales 44-53 (vs. 40-42, 39-42, 39, and 40-44, respectively). H. beni differs from H. virolinica by the number of predorsal scales 17-20 (vs. 10-15). H. beni when compared with H. helleri, overlap somewhat with branched anal-fin ray counts 15-19 (vs. 19-23 for the latter), but can be distinguished from each other by the size of humeral spot 3-4 horizontal series of scales and the total number of vertebrae 38-39 in H. beni (vs. 7-8 in horizontal series of scales and 41-43 vertebrae, respectively for H. helleri) (Ref. 85819).