In this paper, we generated four high-quality genome assemblies, for the first time anchored on genetic maps for apricots, and we sequenced the genomes of 578 accessions from natural populations their whole range (Central Asia and China) and from the two main cultivated populations (European and Chinese cultivated apricots). Withe these data and other available data, we investigated the population structure and divergence history of apricot across Eurasia, as well as the domestication history of cultivated apricots and the selection footprints in genomes. Population structure inferences and approximate Bayesian computation indicated that Chinese and European apricots formed two differentiated gene pools with relatively high genetic diversity, resulting from independent domestication events from distinct wild Central Asian populations, and with subsequent gene flow between wild and cultivated populations. We further detected genomic footprints of selection (i.e., selective sweeps and recurrent changes in amino-acids) in the two groups of cultivated apricots. As expected given the large effective population sizes and outcrossing in fruit trees, we found a relatively low proportion of the genome affected by selection. Different genomic regions showed footprints of selection in European and Chinese cultivated apricots, despite convergent phenotypic traits. Selection footprints appeared more abundant in European apricots, with a hotspot on chromosome 4, while admixture was much more pervasive in Chinese cultivated apricots. In both cultivated groups, the genes affected by selection had predicted functions involved in the perennial life cycle, fruit quality and disease resistance, and/or colocalized with previously mapped genomic regions associated with these functions.