Osteological features of cynodontine species and other characiforms were examined in order to investigate the monophyly of the Cynodontinae and the relationships among its species. A number of derived characters corroborated the hypothesis that the Cynodontinae and its three included genera Cynodon, Rhaphiodon, and Hydrolycus are monophyletic. Hydrolycus armatus is the sister group of H. tatauaia; H. scomberoides is the sister group of the clade formed by the latter two species; and H. wallacei is the sister group of the clade formed by H. armatus, H. tatauaia, and H. scomberoides. Rhaphiodon vulpinus is the sister group to Cynodon, and together they are the sister group to the clade formed by Hydrolycus species.

Three Cynodon Agassiz, 1829, species are diagnosed. Cynodon gibbus Agassiz, 1829, occurs in the Rio Amazonas and Río Orinoco basins, and the Rupununi River, Guyana. Cynodon meionactis Géry et al., 1999, occurs in the upper Maroni River, French Guiana, and C. septenarius, new species, occurs in the Rio Amazonas and its tributaries between the mouths of the Rios Içá and Tapajós, in the Essequibo and Demerara rivers in Guyana, and in the upper portions of the Río Orinoco basin.

Rhaphiodon Agassiz, 1829, is monotypic with R. vulpinus being the most widely distributed cynodontine, its distribution extending to the Río Paraná-Paraguay, and Río Uruguay systems.