Trichomycterus megantoni is readily distinguished from all other members of the subfamily Trichomycterinae from southern South America by having autapomorphic interopercle thickened integument and the presence of foramen frontal-supraoccipital reduced. It is further distinguished from other congeners, with the exception of T. pseudosilvinichthys (Fernández & Vari) and T. yuska (Fernández & Schaefer), by the unique combination of the following features: tip of the pelvic fin when depressed not reaching the anus, premaxillae rectangle, first dorsal fin pterygiophore insertion at or posterior to vertebra 19 to 21,

17 or 19 pairs of ribs on each side, and 37 to 40 vertebrae. T. megantoni can be distinguished from T. yuska and T. pseudosilvinichthys by the presence of a supraorbital canal with pore 3, and an outer tooth row with conic teeth (versus absence pore 3 and distally narrowing incisiform teeth Fernández & Schaefer, 2003; Fernández & Vari, 2004). In addition, the new species is distinguished from T. yuska by head muscles that are not hypertrophied and 17 pairs of ribs on each side (versus head and cheek musculature hypertrophied and 18 or 19 ribs Fernández & Schaefer, 2003); from T. pseudosilvinichthys by the first pectoral fin ray prolonged as thin short filament (versus first pectoral fin ray terminating at the margin of the fin Fernández & Vari, 2004).