Human populations of Central Asian origin have contributed genetic material to northern European populations. It is likely that migrating humans carried livestock to ensure food and ease transportation. Thus, eastern genes could also have dispersed to northern European livestock populations. Using microsatellite data, we here report that the essentially different genetic distances DA and (deltamu)2 and their corresponding phylogenetic trees show close associations between the Mongolian native horse and northern European horse breeds. The genetic distances between the northern European breeds and Standardbred/Thoroughbred, representing a southern-derived source of horses, were notably larger. We suggest that contribution of genetic material from eastern horses to northern European populations is likely to have occurred.