Modern horses, zebras, and asses belong to the genus Equus, the only surviving genus in a once diverse family, the Equidae. Based on fossil records, the genus appears to have originated in North America about 4 million years ago and spread to Eurasia (presumably by crossing the Bering land bridge) 2 to 3 million years ago. Following that original emigration, there were additional westward migrations to Asia and return migrations back to North America, as well as several extinctions of Equusspecies in North America.
The last prehistoric North American horses died out between 13,000 and 11,000 years ago, at the end of the Pleistocene, but by then Equus had spread to Asia, Europe, and Africa.
Animals that on paleontological grounds could be recognized as subspecies of the modern horse originated in North America between 1 million and 2 million years ago. When Linnaeus coined the species name, E. caballus, however, he only had the domesticated animal in mind. Its closest wild ancestor may have been the tarpan, often classified as E. ferus; there is no evidence, though, that the tarpan was a different species. In any case the domesticated horse probably did not arise at a single place and time, but was bred from several wild varieties by Eurasian herders.
 
In recent years, molecular biology has provided new tools for working out the relationships among species and subspecies of equids. For example, based on mutation rates for mitochondrial DNA (mtDNA) Ann Forstén, of the Zoological Institute at the University of Helsinki, has estimated that E. caballus originated approximately 1.7 million years ago in North America. More to the point is her analysis of E. lambei, the Yukon horse, which was the most recent Equus species in North America prior to the horse's disappearance from the continent. Her examination of E. lambei mtDNA (preserved in the Alaskan permafrost) has revealed that the species is genetically equivalent to E. caballus. That conclusion has been further supported by Michael Hofreiter, of the Department of Evolutionary Genetics at the Max Planck Institute in Leipzig, Germany, who has found that the variation fell within that of modern horses.
These recent findings have an unexpected implication. It is well known that domesticated horses were introduced into North America beginning with the Spanish conquest, and that escaped horses subsequently spread throughout the American Great Plains.