Hemigrammus tocantinsi differs from most congeners [except H. bellottii (Steindachner), H. bleheri Géry & Mahnert, H. boesemani Géry, H. brevis Ellis, H. cylindricus Durbin, H. cupreus Durbin, H. erythrozonus Durbin, H. geisleri Zarske & Géry, H. levis Durbin, H. mahnerti Uj & Géry, H. microstomus Durbin, H. mimus Böhlke, H. orthus Durbin, H. rhodostomus Ahl, H. rodwayi Durbin, H. tridens Eigenmann, H. skolioplatus Bertaco & Carvalho, and H. vorderwinkleri Géry] by the number of branched anal-fin rays, 15-17 (vs. less than 15 in H. analis Durbin, H. hyanuary Durbin, H. iota Durbin, and more than 17 on remaining species). From the species with the same range of branched anal-fin rays, Hemigrammus tocantinsi differs by the presence of 1-2 (mode 1) maxillary teeth (vs. 3-11 in H. bellottii, H. cylindricus, H. cupreus, H. mimus, and H. skolioplatus); longitudinal stripe posteriorly broad, larger than one scale depth or than pupil diameter (vs. thinner than one scale depth or pupil diameter or longitudinal stripe absent in H. bellottii, H. boesemani, H. brevis, H. erythrozonus, H. geisleri, H. levis, H. mahnerti, H. microstomus, H. orthus, H. rodwayi, H. tridens, and H. vorderwinkleri); caudal-fin lobes hyaline (vs. presence of a conspicuous broad black marginal or submarginal band across the distal part of caudal-fin lobes in H. bleheri and H. rhodostomus). Furthermore, Hemigrammus tocantinsi can be distinguished from all congeners by the color pattern of live specimens (reddish or orange in male and yellowish pigmented in female).