This species is distinguished from its congeners, except for G. pantanal, in possessing the following characteristics: a unique pigmentation pattern comprising a uniform dark brown background with prominent broad whitish or yellowish posteriorly inflected bands with dark margins, which narrow dorsally in the anterior portion of the body until they completely fade at around the position of the lateral line, never reaching or traversing the dorsal surface of the body; differs from G. pantanal in possessing 2 (vs. 1) adjacent, posteriorly facing, preopercular-mandibular sensory canal pores in the dorsoposterior portion of the preopercle. This species belongs in the G. carapo species group while G. pantanal belongs to the G. pantherinus species group. Gymnotus capanema is further distinguished from G. pantanal in possessing fewer anal-fin rays (180-205 vs. 235-280), has a deeper body (9.6-10.1% LTvs. 8.0-9.5% TL), and fewer pectoral-fin rays (11-15 vs. 16-18).

Gymnotus capanema also differs unambiguously from all other species of the G. carapo species group from the Amazon Basin and north-east Brazil, except G. curupira, G. chaviro and G. varzea, in possessing a short head (8.5-9.3% TL vs. 9.7-14.2% TL); differs from G. curupira in possessing a deeper body (9.6-10.0% TL vs. 7.4-8.6% TL), larger preorbital distance (36.4-49.7% HL vs. 34.3-36.0 HL), fewer pectoral-fin rays (11-15 vs. 16-17), fewer pored lateral-line scales to the first ventral ramus (47-56 vs. 59-62) and the distinct pigmentation reported here; from G. chaviro in possessing fewer pectoral-fin rays (12-15 vs. 18-19) and fewer anal-fin pterygiophore scale rows (5-8 vs. 12-13); from G. varzea in possessing a larger preorbital distance (36.4-49.7% HL vs. 29.7-35.8% HL), fewer anal-fin rays (180-205 vs. 230-310), fewer pectoral-fin rays (11-15 vs. 16-19) and the distinct pigmentation reported in the species description (Ref. 89487).