Przewalski’s horses (PHs, Equus ferus ssp. przewalskii) were discovered in the Asian steppes in the 1870s and represent the last remaining true wild horses. PHs became extinct in the wild in the 1960s but survived in captivity, thanks to major conservation efforts. The current population is still endangered, with just 2,109 individuals, one-quarter of which are in Chinese and Mongolian reintroduction reserves 1. These horses descend from a founding population of 12 wild-caught PHs and possibly up to four domesticated individuals 2–4. With a stocky build, an erect mane, and stripped and short legs, they are phenotypically and behaviorally distinct from domesticated horses (DHs, Equus caballus). Here, we sequenced the complete genomes of 11 PHs, representing all founding lineages, and five historical specimens dated to 1878–1929 CE, including the Holotype. These were compared to the hitherto-most-extensive genome dataset characterized for horses, comprising 21 new genomes. We found that loci showing the most genetic differentiation with DHs were enriched in genes involved in metabolism, cardiac disorders, muscle contraction, reproduction, behavior, and signaling pathways. We also show that DH and PH populations split ∼45,000 years ago and have remained connected by gene-flow thereafter. Finally, we monitor the genomic impact of ∼110 years of captivity, revealing reduced heterozygosity, increased inbreeding, and variable introgression of domestic alleles, ranging from non-detectable to as much as 31.1%. This, together with the identification of ancestry informative markers and corrections to the International Studbook, establishes a framework for evaluating the persistence of genetic variation in future reintroduced populations. Display omitted •Complete genomes were sequenced for 21 domesticated and 17 Przewalski’s horses•Selection signatures and variants specific to Przewalski’s horses were detected•Domesticated and Przewalski’s horse ancestors mixed post-divergence ∼45,000 years ago•Captivity increased inbreeding and domestic introgression in Przewalski’s horses Der Sarkissian et al. characterized complete genomes of modern and historical Przewalski’s horses, a wild and endangered population distinct from domesticated horses. Comparative analyses revealed specific signatures of selection, increased inbreeding, and variable introgression from domesticated horses in the last 110 years in captivity.