This study was the first to analyze the polymorphic characteristics of a wide range of biochemical markers in aboriginal Yakut horses. A total of 124 alleles, including 48 alleles of seven blood-group loci and 76 alleles of ten loci for enzymes and other proteins, were studied. For these polymorphic systems, a computer analysis of the genetic distances between 85 horse breeds of different origin from all parts of the world was performed. The low level of hereditary variation in the Yakut horses confirmed that this breed is old and has long been an isolated population. Phylogenetic analysis demonstrated that Yakut horses exhibited the most genetic similarity to the breeds from the Central Asian cluster, such as Akhal Teke, Arabian, Yabou, and Caspan Pony (Iran). The dispersal route of ancient horses was revealed. It led from America through Siberia and Central Asia to Africa and Eastern Europe, where evidence of the earliest domestication of horses was found. Genetic and ecological explanations of the formation of racing and draft breeds with similar immunogenetic characteristics are advanced. These explanations agree with craniological data on fossils and with the relative rates of growth of the axial and peripheral skeletons in modern breeds. These data shed light on the initial stages of domestication of the horse, an event that was extremely important for development of the human civilization.