Rhinoceroses are among the most endangered mammalian species today. Their past diversity is well documented from the Eocene onward, although their evolutionary history is far from being fully understood. Here, we elucidate the systematic affinities of a Pleistocene rhinoceros species represented by a partial skeleton from 709±68 ka archaeological deposits in Luzon Island, Philippines. We perform a comprehensive phylogenetic analysis including all living species and a wide array of extinct rhinocerotid species. We confirm the early split between Elasmotheriinae and Rhinocerotinae at c 35.5 Ma and constrain the divergence between recent Asian and African rhinoceroses at c 24 Ma, with contrasting phenotypic evolutionary rates in Diceroti and Rhinoceroti. Dental features reveal the existence of an unsuspected Asian Pleistocene clade, referred to as Nesorhinus gen. nov. It includes the rhinoceros from the Philippines and another extinct species from Taiwan, N. hayasakai. Nesorhinus is sister group to a cluster comprising Dicerorhinus and Rhinoceros. Our phylogenetic results strongly suggest an island-hopping dispersal for Nesorhinus, from Asian mainland towards Luzon via Taiwan by late Miocene times or later, and Pleistocene dispersals for representatives of Rhinoceros. Nesorhinus philippinensis would be the first perissodactyl species supporting the island-rule hypothesis, with decreased body weight and limb-bone robustness.