The genus Aphyodite has a complex taxonomic history. It was described as monotypic, and the only diagnosis provided was “an Aphyocharax with a scaled caudal fin”. After the description, the genus was revised twice, but some morphological inconsistences remained, pending a proper morphological analysis. Currently, Aphyodite is a member of Aphyoditeinae and can be distinguished from all the other representatives of this subfamily by having the first infraorbital with a conspicuous sensory canal not reaching the anterior edge of the bone. During the revision of the genus, two new species were found: Aphyodite apiaka, new species, from the Rio Madeira basin, that can be diagnosed from its congeners by the length of the first infraorbital sensorial canal, which is longer than half length of bone; and Aphyodite tupebas, new species, from the Rio Solimões basin, that can be diagnosed from its congeners by the possession of only conical teeth in the premaxilla.