The horse is one of the last large mammals to be domesticated, but probably the one that most impacted human history, by providing both primary products, such as meat and hide, and secondary products of unmatched importance, fast transportation. The horse significantly increased farmland productivity when employed in agriculture; changed the economic and social aspects of herder’s lives; facilitated the continental scale trade and the spread of human populations, diseases, languages and cultures; and changed the way we made war. Despite of key interest to archeologists, historians and agronomists, the process of early horse domestication, and its further developments during history, remain highly contentious, including in the number and location of candidate domestication centre(s). The oldest unambiguous archeological evidence for horse domestication is found in the 5,500-year-old Botai culture of the Central Eurasian steppe, in present-day Northern Kazakhstan. Harnessing the power of ancient genomics, this PhD project aimed at understanding the origin and process of horse domestication by generating the largest ancient genome time series hitherto available for a non-model organism. In the last three years, we have shown that Botai horses do not represent the main ancestral population of modern domesticates but instead that of Przewalski’s horses. The latter thus represent the feral descendants of the earliest domestic horses in the archaeological record rather than true wild horses, as commonly thought. We have also shown that the wild archaic Iberian horses only contributed marginally to the genetic makeup of modern horses, and ruling out Iberia as an independent domestication centre for horses. In addition to revisit early domestication centre(s), we have identified an extinct lineage of wild horses in Siberia, which existed until the time of horse domestication but left no genetic trace in modern horses. Furthermore, while investigating the demographic trajectories of horse population, we found that two major events reshaped the genetic structure of horse domesticates during recent historical time periods. Firstly, the onset of modern breeding ~200 years ago tremendously impacted patterns of horse genetic diversity. Additionally, we have identified the growing influence of Persian-related horse lineages into European and Asian horse populations, starting around the 7th-9th centuries AD.