It is known from one species, Phanagoroloxodon mammontoides, which is described from a partial skull from Russia, of probable Late Pliocene-Early Pleistocene age.

[1][2] The holotype of Phanagoroloxodon was found on the banks of the Psekups river in the northwestern Caucasus of Russia, and was given to the Krasnodar State Historical and Archaeological Memorial Museum-Reserve by I.N.

[1][2] Other possible remains of the species include molar teeth described from the nearby Sinyaya Balka site near the eastern shore of the Sea of Azov.

[3] In 2005, a second species Phanagoroloxodon irtyshensis was described based on a skull found near Pavlodar in Kazakhstan, but this may represent a specimen of the steppe mammoth (Mammuthus trogontherii).

Like Elephas, the top of the skull has a saddle-like groove running along the midline and the nasal process is rounded.