Characidium helmeri is distinguished from other species of Characidium by possessing dark, vertically elongated, irregular, narrow spots or dashes, usually more evident over the midlateral stripe and/or ventral half of body, formed by high concentration of melanophores on the posterior half of scales, occurring in a somewhat curved or zigzag-shape. It also differs from congeners by having extremely reduced or complete absence of supraorbital. It further differs by having lateral line reduced (vs. complete, except in C. bahiense, C. interruptum, C. laterale, C. mirim, C. nupelia, C. rachovii, C. stigmosum and C. xavante), adipose fin absent (vs. present, except in C. mirim, C. nupelia, C. stigmosum, and C. xavante), and isthmus naked on its anteriormost portion (vs. isthmus completely covered by scales in most congeners, except in C. alipioi, C. boavistae, C. crandellii, C. declivirostre, C. fasciatum, C. gomesi, C. grajahuensis, C. japuhybense, C. lauroi, C. macrolepidotum, C. oiticicai, C. schubarti, C. timbuiense, and C. vidali). It can be diagnosed from C. bahiense, C. interruptum, C. laterale, C. mirim, C. nupelia, C. rachovii and C. xavante by having more pored lateral line scales 13-22 (vs. 5-11) and two series of dentary teeth (vs. one). It can be further separated from C. nupelia and C. xavante by the absence of a dark humeral blotch (vs. presence) smaller number of dark vertical bars on the body, 7-12 when present (vs. 12-18). It is distinct from C. vestigipinne, a species with adipose fin absent or reduced, by having two dentary rows of teeth, the outer with tricuspid teeth (vs. one row of conical teeth), 4 scales above lateral line and 4 below (vs. 5 above; and 5 or 6 below), and absence of roundish black marks on pelvic, dorsal, and anal fins (vs. presence). It further differs from C. stigmosum by having a black basicaudal dot (vs. absence), and by having pelvic, pectoral, anal, and caudal fins not dark pigmented in males (vs. pigmented) (Ref. 104900).

Description: Dorsal-fin rays ii,9, ii,10, iii,9 or iii,10. Anal-fin rays ii,5 or ii,6; iii,6. Pectoral-fin rays 8-12 total rays, number of unbranched rays highly variable; unbranched anterior rays ii, iii, iii, iv, ix and posteriormost rays varying from by 1-4 unbranched; one specimen with all rays unbranched. Pelvic-fin rays highly variable, i,4,iii, i,4,iv, i,5,i , i,5,ii, i,5,iii, i,6,i, i,6,ii, ii,6,ii, i,7, i,7,i, or i,8,i (Ref. 104900).