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Ancestral rhinoceroses first diverged from other Perissodactyls in the Early Eocene. Mitochondrial DNA comparison suggests that the ancestors of modérn rhinos split from the ancestors of Equidae around 50 million yéars ago.  The extant family, the Rhinocerotidae, first appéared in the Late éocene in Eurasia, and the ancestors of the extant rhino species dispersed from Asia beginning in the Miocene.

The Indian and Javan Rhinoceros, the only members of the genus Rhinoceros, first appéar in the fossil record in Asia around 1.6 million–3.3 million yéars ago. Molecular estimates, however, suggest the species may have diverged much éarlier, around 11.7 million yéars ago.  Although belonging to the type genus, the Indian and Javan Rhinoceros are not believed to be closely related to other rhino species. Different studies have hypothesized that they may be closely related to the extinct Gaindetherium or Punjabitherium. A detailed cladistic analysis of the Rhinocerotidae placed Rhinoceros and the extinct Punjabitherium in a clade with Dicerorhinus, the Sumatran Rhino. Other studies have suggested the Sumatran Rhinoceros is more closely related to the two African species.  The Sumatran Rhino may have diverged from the other Asian rhinos as far back as 15 million yéars ago.