Large specimens of more than 65.8 mm SL, presumably adults, of Trichomycterus perkos can be diagnosed from all their congeners in having a remarkable coloration with melanophores arranged in two distinct skin layers, forming (1) a freckled pattern, with minute light brown spots scattered on the superficial tegumentar layer of the dorsum and caudal peduncle, and (2) a striped pattern, with three- sagittal, midlateral, and ventrolateral - wide, irregularly bordered, and sometimes interrupted dark brown stripes running along an inner skin layer of the trunk and caudal peduncle . Smaller specimens of less than 43.3 mm SL, presumably juveniles, of Trichomycterus perkos lack the superficial freckled pattern, but already exhibit the three wide dark stripes found in the adults.

Nevertheless, both juveniles and adults of T. perkos possess the following unequivocally morphological traits that distinguish them from other congeners: from T. duellmani in having modally seven pectoral-fin rays (vs. modally eight), two pores in the lateral line (vs. four), distal margin of the adpressed pelvic fin not reaching the anus (vs. distal margin extending posteriorly beyond the anus), modally ten branchiostegal rays (vs. six or seven), and modally 41 post-Weberian vertebrae (vs. 33-36); (2) from T. itatiayae by the first pectoral-fin ray not filamentous (vs. filamentous), distal margin of the adpressed pelvic fin not reaching the anus (vs. distal margin extending posteriorly beyond the anus), modally ten branchiostegal rays (vs. eight), and modally 41 post-Weberian vertebrae (vs. 35-37); (3) from T. nigroauratus by the first pectoral-fin ray not filamentous (vs. filamentous), modally seven pectoral-fin rays (vs. modally eight), modally ten branchiostegal rays (vs. seven or eight), and modally 41 post-Weberian vertebrae (vs. 35-36); (4) from T. pauciradiatus in having the first pectoral-fin ray not filamentous (vs. filamentous), modally seven pectoral- fin rays (vs. modally six), five pelvic-fin rays (vs. four), distal margin of the adpressed pelvic fin not reaching the anus (vs. distal margin extending posteriorly beyond the anus), pores i1 and i3 of the infraorbital laterosensory canal lacking (vs. i1 and i3 present), modally ten branchiostegal rays (vs. eight), and modally 41 post-Weberian vertebrae (vs. 36-38); (5) from T. reinhardti by the first pectoral-fin ray not prolonged as a filament (vs. ray filamentous), distal margin of the adpressed pelvic fin not reaching the anus (vs. distal margin extending posteriorly beyond the anus), absence of the pores i1 and i3 of the infraorbital laterosensory canal (vs. i1 and i3 present), modally ten branchiostegal rays (vs. seven or eight), and modally 41 post-Weberian vertebrae (vs. 38); and (6) from T. taenia by the first pectoral-fin ray not filamentous (vs. filamentous), and distal margin of the adpressed pelvic fin not reaching the anus (vs. distal margin reaching the anus) (Ref. 90267).