Trichomycterus wapixana is distinguished from all congeners of Trichomycterus hasemani group by having 34 to 36 vertebrae (vs. 32 in T. hasemani and T. johnsoni, 29 to 32 in T. anhanga) and anal-fin origin in a vertical through the base of the 20th, 21st or 22nd vertebra (vs. 18th in T. hasemani, 17th in T. johnsoni and 16th in T. anhanga). It differs from T. hasemani and T. johnsoni by having the origin of the pelvic fin in a vertical between the base of 15th and 17th vertebrae (vs. 14th in T. hasemani and 13th in T. johnsoni) and a dark spot on the middle of the lower lip (vs. absent). It is distinguished from T. anhanga by having pelvic fins and girdle (vs. absent), 10 to 11 dorsal procurrent rays in the caudal fin (vs. 6 to 8), 9 to 12 ventral procurrent rays in the caudal fin (vs. 6 to 7), seven (ii +5 or iii + 4) anal-fin rays (vs. ii + 4), five (i + 4 or ii + 3) pectoral fin rays (vs. i + 2), dorsal-fin origin at vertical through the base of the 20th, 21st or 22nd vertebra (vs. 16th or 17th), 6 branchiostegal rays (vs. 4 or 5), two pairs of pleural ribs on first two vertebrae posterior to Weberian Complex (vs. single pair), a series of dark brown spots in the lateral midline of the body (vs. absent), broad palatine (vs. narrow, comma-shaped palatine), and parasphenoid present (vs. absent). It can be separated further from T. johnsoni by the origin of the urogenital pore in a vertical between the base of the 17th and 19th vertebrae (vs. 15th) (Ref. 116786).