Ceratotherium is more closely related to the genus Diceros (which contains the black rhinoceros) than it is to other living rhinoceroses, with the clade containing the two comprising the tribe Dicerotini (also spelled Diceroti) or subtribe Dicerotina.

Some authors have alternatively assigned the Pliocene East African remains to the species Ceratotherium efficax.

[4] Some authors have considered Ceratotherium mauritanicum to be the ancestor of the living white rhinoceros if the Pliocene East African material is included, though others who only include North African material have suggested that it instead represents a distinct offshoot not ancestral to the white rhinoceros.

[6][5] The placement of "Ceratotherium" neumayri from the Late Miocene of Europe and Western Asia within the genus has been questioned, with it possibly more closely related to the black rhinoceros or ancestral to both the white and black rhinoceros, or an early offshoot away from these two species, with other authors assigning it to Diceros or to the monotypic genus Miodiceros.

[7] The species "Ceratotherium" douariense, known from the late Miocene of Tunisia, dating to around 7 million years ago, has been assigned to the genus by some authors.