Abstract: The purpose of the work was to explore the athletics-related genes of Mongolian horse at genome level. Based on whole-genome sequencing technology, the blood of Mongolian horse was sampled and sequenced. The specific genes and positive selection genes of Mongolian horse were further detected combined with the mammalian genome databases of 7 species including human, bovine, mouse, etc.. The 19 475 annotated protein-coding genes were obtained via data analysis, while 38 specific genes and 45 positive selection genes were screened in Mongolian horse. By GO enrichment, KEGG pathway enrichment analyses and previous studies, the 17 protein-coding genes of positive selection including MAPK13, CCN2, FSCN3, BTG1 and TF, etc. were considered to be probably involved in athletic performance of Mongolian horse. The biological functions of the above 17 protein-coding genes contained actin filament organization, positive regulation of cardiac muscle contraction, calcium ion binding, regulation of intracellular pH, angiogenesis, positive regulation of collagen biosynthetic process, etc.. The mRNA 3'UTR of MAPK13, LOC100057755, EHD4, MICAL3, TMBIM1 and F11R were targeted by 7 miRNAs (such as eca-miR-302c, eca-miR-8974, eca-miR-9077, etc.). The above athletics-related protein-coding genes of positive selection can make people comprehend athletics character of Mongolian horse, while also provide molecular theoretical basis for targeting competitive livestock breeding.