Among all domesticates, the horse can confidently be considered as the animal that most impacted the history of human dynamics. Once they domesticated the horse, human civilizations got hold of essential primary domestication products including meat and milk, but also invaluable secondary products, such as fast transportation and powerful workforce.The horse thus deeply enhanced the circulation of people, goods, culture and ideas, promotin gthe spread of vast military and political units across Eurasia up until the 1900s. The various steps underpinning horse domestication are however difficult to track in the archaeological record and still poorly understood based on patterns of DNA variation among modern breeds. In the last decade, the advent of ancient genomics has revolutionized evolutionary biology by providing a direct window into the past history of populations. Ancient genomics therefore provides the necessary time travel machine to investigate the key historical transition in the history of humankind that was induced by the horse domestication. Leveraging the latest breakthroughs in ancient DNA recovery and High-Throughput sequencing technologies, this PhD project aimed at deciphering the genetic changes underlying the horse domestication process by generating the largest ancient genome dataset for a non-human organism, spanning the whole temporal and geographic range of horse domestication. This dataset revealed that horses first herded at Botai in Northern Kazakhstan ~5,500 years ago are not the ancestors of modern domestic horses but instead of modern Przewalski’s horses, previously thought to represent last true wild population on Earth. This major discovery also suggests that a swift genomic replacement in the domestic stock took place in the third millennium BCE, probably contributing to precipitating humankind into a new metal era, the Bronze Age. Additionally, this PhD work identified the genetic signatures associated with different management strategies and the evolutionary dynamics at play within distinct domestication stages. Inparticular, we were able to rule out Iberia as a major contributor to the modern domestic st ock and moving towards more recent times, we characterized the growing influence of Persianlike horses starting in the early Middle Ages.