A new small to medium-sized hippopotamus, Hexaprotodon lothagamensis is described from the late Miocene of northern Kenya. The material was recovered from Lothagam, a site southwest of Lake Turkana. This narrow-muzzled hippopotamus differs from other Hexaprotodon species in terms of its small size and shallow symphysis. The six incisors are arranged in a straight line across the front of the jaw and the lower canines are almost aligned with the cheek tooth row. H. lothagamensis compares more closely to an Arabian species, Hexaprotodon aff. H. sahabiensis from the late Miocene, than to any other African Hexaprotodon. The phylogeny of the Hippopotamidae is discussed and although the genera names are maintained, the genus Hexaprotodon is paraphyletic. Hexaprotodon lothagamensis appears to be less derived than the extant pygmy hippopotamus, H. (Choeropsis) liberiensis, which was previously considered to be a living fossil.