Gymnotus capitimaculatus belongs to the Gymnotus pantherinus species-group, characterized by having a slender body (body depth 7.2-8.9 % of TL), proximal portion of the fifth rib with broad triangular ridge, more than three times width of the sixth rib (vs. narrow ridge, less than three times width of the sixth rib) and one laterosensory pore in the dorso-posterior portion of the preopercle, in the preopercular-mandibular canal (vs. two pores). It differs from all congeners by having a pair of round blotches anteriorly positioned or under vertical passing through eye, on ventral portion of the head. It can be diagnosed from all members of the G. pantherinus species-group (sensu) by the following unique combination of characters: tail with a unique series of bands or round spots (vs. tail with randomly disposed spots, never forming a unique series); precaudal portion of the trunk lacks bands or with rounded and/or vermiculated spots scattered all over it (vs. with well defined bands); 45 precaudal vertebrae (vs. 31-43 or 46-51); 9 scales above lateral line at mid-body (vs. 6-8 or 10); anal fin base length 75.2-78.6 % of TL (vs. 62.9-74.7 or 79-83.8 %); anus-anal fin length 101.4-122.8 % of HL (vs. 50-96.3 %); and branchial opening 38.5-45.0 % of HL (vs. 24-35) (Ref. 96661).