Moenkhausia rubra can be diagnosed from all congeners, except M. hemigrammoides and M. nigromarginata, by having dark pigmentation on the anteriormost rays of dorsal and anal fins. It differs from M. hemigrammoides and M. nigromarginata by having 17-20 branched rays on anal fin (vs. 20-22 in M. nigromarginata and 22-25 in M. hemigrammoides). It can be further distinguished from M. hemigrammoides by its dark blotch on the caudal peduncle extending to middle caudal-fin rays (vs. absence) and from M. nigromarginata by the lack of dark pigmentation on the anteriormost pelvic fin rays (vs. dark pigmentation present), dark pigmentation absent along the distal margin of anal fin (vs. presence) and lack of longitudinal black zigzag stripes between longitudinal rows of scales on body (vs. presence). It differs further from its congeners by the combination of the following characters: 5 or 6 scale rows above lateral line, 4 or 5 scale rows below the lateral line; 17-20 branched rays on anal fin; 33-34 scales on lateral line; 3-6 maxillary teeth; one round humeral spot; absence of reticulated color pattern on body; absence of a dark broad stripe extending from the opercle to the caudal peduncle; distal portion of caudal-fin lobes hyaline; and dark caudal-peduncle spot extending posterior to the middle caudal-fin rays (Ref. 96859).