Characidium nana is diagnosed from all other species of Characidium, except C. bahiense, C. interruptum, C. laterale, C. mirim, C. nupelia, C. rachovii, C. stigmosum, and C. xavante by having short, incomplete lateral line, the lack of the inner dentary series of teeth, and the absence of the parietal branch of the supraorbital laterosensory canal. It differs from C. bahiense, C. interruptum, C. laterale and C. rachvoii by the absence of the adipose fin (vs. presence of adipose fin); from Characidium mirim and C. stigmosum by having a conspicuous dark blotch onto the caudal peduncle (vs. absence of caudal blotch); and from C. nupelia and C. xavante by possessing a broad, conspicuous dark midlateral stripe (vs. narrow, inconspicuous midlateral stripe). It is further distinguished from C. xavante by having 12 circumpeduncular scales (vs. 10) (Ref. 104905).