“Apteronotus” bonapartii (Castelnau 1855) was described based on a single specimen caught in a lake draining into the Río Ucayali, Perú, and is now reported from several rivers in South America. Because the generic placement of this species is currently uncertain, in this paper we use the genus name “Apteronotus” within quotes for reference to “Apteronotus” bonapartii (Castelnau, 1855) and “A.” apurensis Fernández-Yépez, 1968; we use the genus name without quotes for the more precise usage referring to a putatively monophyletic group including the type species (A. albifrons). “Apteronotus” bonapartii has a laterally compressed body, subterminal mouth with the rictus passing the eyes and teeth present in both jaws. The species has been differentiated from others placed in the genus by the low number of scale rows (5–8) above the lateral line. There is substantial intraspecific variation among specimens, in part associated with pronounced sexual dimorphism in head shape. We describe aspects of the morphology and cranial osteology of 52 specimens of “A.” bonapartii from Central Amazon and 12 specimens from other localities in the Amazon and Orinoco basins including the holotype from Río Ucayali. Males have slightly longer facial dimensions than females, and the holotype appears to fit on the male growth trajectory. Specimens from Napo, Metica, Orituco and Apure rivers are similar to specimens from the Central Amazon and the holotype. There is sexual dimorphism in the structure of the lower jaw, including its overall shape and profile (e.g., smooth curve of the dentary in males vs. a straight edge of the dentary in females), but no sexual dimorphism of teeth was noted. The postarticular portion of the lower jaw is formed equally by the anguloarticular and retroarticular. There is individual variation in the ossification of pharyngobranchial 4 and hypobranchial 4. We found no morphological differences between specimens of “A.” bonapartii from the Río Apure and the species described as “A.” apurensis Fernández-Yépez 1968.