Abstract: Domestication, natural selection, and artificial selection will leave selection signals on the genome. Studying these selection signals is one of the important strategies for screening functional genes. Based on the resequencing data of Wild yak（Bos mutus） and Tianzhu white yak（Bos grunniens）, GATK（genome analysis toolkit） was uesd to obtain SNP（single nucleotide polymorphisms） mutation sites, and then the population differentiation index F_ST and Tajima’s D method were uesd to analyze the selection signal distribution of the two yak populations in the study. The top 5% of the F_ST value and the top 2.5% at both ends of the Tajima’s D value（top 2.5% and bot 2.5%） were selected as the selection threshold, and the sites beyond the threshold were defined as strong selection signal sites. After gene annotation by SnpEff, 868 candidate genes were detected by the F_ST method. These genes were enriched in some GO items related to muscle, such as positive regulation of cell proliferation, actin cytoskeleton organization, and magnesium ion binding. The analysis of KEGG showed that these genes were involved in muscle development and hypoxia adaptation, including MAPK signaling pathway, actin cytoskeleton regulation, PI3 K-Akt signaling pathway, ECM receptor interaction, cell cycle, and Rap1 signaling pathway. The results of Tajima’s D analysis showed that 377 214（Tajima’s D＞1.974 72） and 539 869（Tajima’s D＜-1.780 03） loci were detected from the Tianzhu white yak genome, and 38 and 22 candidate genes were annotated, respectively. In the wild yak genome, 413 240（Tajima’s D＞1.854 31） and 332 871（Tajima’s D＜-1.512 31） loci were detected, and 30 and 24 candidate genes were annotated, respectively. After annotating the overlap sites of strong selection signals screened by the two methods, 90 and 83 candidate genes were obtained from the genomes of wild yak and Tianzhu white yak, respectively. Two domestication-related genes（SCRIB1, SNCA）, one gene related to hypoxia adaptation（THADA）, and two genes related to hair color（MAPK3, NNT） were selected from these candicate genes. In this study, a series of genes and pathways related to genetic differentiation and phenotypic differences in wild yak and Tianzhu white yak were screened by F_ST and Tajima’s D method, which provides a theoretical basis for further studying the relationship between the yak genome and phenotype, and determining the genes that control important economic traits of the yak.