Phylogenetic analysis of six species of late Cenozoic Tapirus from North America and the three extant Neotropical species of Tapirus using 64 informative characters and three to five outgroups reveals strong support for a monophyletic Tapirus, and several subgroups within the genus. Tapirus johnsoni (late Miocene) consistently falls outside crown-clade Tapirus and is the sister taxon of the remaining eight species in the genus. "Tapiravus" polkensis (late Miocene-earliest Pliocene) is a member of crown-clade Tapirus and is referred to Tapirus. It is a member of a strongly supported clade that includes Tapirus bairdii and Tapirus veroensis. Members of this clade share a triangular-shaped interparietal, a deep, extensive fossa for the meatal diverticulum on dorsal surface of nasal, broad and flat posterior lacrimal process, and posterolaterally oriented lambdoidal crests.
The Tapirus terrestris-T. pinchaque clade shares a reduced (or lost) interparietal, shortened posterior process of the premaxilla, and a well developed anterior lacrimal process. Tapirus webbi (late Miocene of Florida) may be an early member of this clade, but current evidence is equivocal.
The results of the morphology-based parsimony analysis are in agreement with those of a molecular-based analysis with regards to the interrelationships of extant Neotropical species and a Miocene divergence between T. terrestris and T. bairdii.