The mountain tapir belongs to a very ancient order of mammals known as Perissodactyla, whose origin dates back to around 60 million years ago, a few million years after the extinction of dinosaurs. To this group of mammals, besides the tapirs, belong the modern rhinoceroses and equids (donkeys, horses and zebras). The oldest fossil remains of tapirs date back to the Lower Eocene (55 MYA). These fossils show very similar characteristics to those of modern tapirs, so they are considered to be living fossils.

All tapirs are part of a single family (Tapiridae) and genus (Tapirus). The family Tapiridae and the genus Tapirus, according to the fossil record, had their origin in the Oligocene of Europe (33-37 MYA). Tapirs have inhabited Europe as well as Asia and America, although in Europe they disappeared during the Pleistocene. In America, the genus Tapirus has been present from the Middle Miocene in North America, to the present, in Central and South America. As for Asia, the fossil record indicates that tapirs have existed there from the early Miocene to the present.

In the three continents where tapirs have existed, about twenty species have been identified, of which only four are recognized to exist at present: The Malayan tapir (Tapirus indicus), which inhabits Southeast Asia, the Baird’s or Central American tapir (Tapirus bairdii), which inhabits Central America and northwestern Colombia, the lowland tapir (Tapirus terrestris) which inhabits the entire Amazon basin and the Orinoco region, with isolated populations in the Colombian Caribbean, and the mountain or Andean tapir (Tapirus pinchaque) which inhabits the high Andes of northwestern South America. The existence of a fifth Amazonian species called  Tapirus kabomani is controversial and has not been officially recognized by the IUCN.

It has been proposed that the mountain tapir evolved in northern South America after the common ancestor of this species and the lowland tapir entered through the Isthmus of Panama about three million years ago when the connection between the north and south of the continent occurred in what is known as the Great American Biotic Interchange (GABI). There is evidence that after the GABI occurred, the Andes underwent a pronounced uprising, which would suggest that the common ancestor of the South American tapir split off to give rise to the lowland tapir and the Andean or mountain tapir. 

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