Although little is known about Kenyapotamus, its dental pattern bore similarities to that of the genus Xenohyus, a European suid from the Early Miocene.

This led some scientists to conclude that hippopotami were most closely related to modern peccaries and suids.

[2] Recent molecular research has suggested that hippopotamuses are more closely related to cetaceans than to other artiodactyls.

A morphological analysis of fossil artiodactyls and whales, which also included Kenyapotamus, strongly supported a relationship between hippos and the anatomically similar family Anthracotheriidae.

Two archaic whales (Pakicetus and Artiocetus) formed the sister group of the hippopotamid-anthracotheriid clade, but this relationship was weakly supported.