Abstract: The purpose of this study is to explore the selected genes related to the body size of Lepus yarkandensis and to provide a reference for the identification of major genes associated with ontogeny and growth. Based on the SLAF-Seq（Specific-locus amplified fragment sequencing） technology. The selective sweep method was carried out on 11 large-sized Lepus tolai and 15 small-sized Lepus yarkandensis in this study. The selected genes were annotated and enriched by GO and KEGG, and the body size genes of Lepus yarkandensis were identified. The results showed that a total of 439 420 SNPs were selected according to the 95% quantile of the F_st value and π ratio(F_st＞0.566, π ratio＞5.80). 1 943 candidate genes were involved in these loci by SNP annotation. The results of KEGG enrichment analysis indicated that ubiquitin mediated proteolysis, mTOR（Mammalian target of rapamycin）, and Wnt signaling pathway may be correlated with the body size of Lepus yarkandensis. The enrichment analysis of KEGG and GO showed that 25 candidate genes may be connected with the body size of Lepus yarkandensis, and these genes were relevant to bone and muscle formation and growth, fat metabolism, energy generation, cell proliferation, cell apoptosis, and organ size. Other animal research reported that the candidate genes such as PTEN, WNT1, WNT7 A, FGF13, RPS6 KB1, RRAGA, and GANC may be concerned with the body size of animals, and some of them were enriched in the related pathways that regulated body size. These genes may play an important role in controlling the body size of Lepus yarkandensis and may serve as key candidate genes which influence the small-sized Lepus yarkandensis. The results of this study provide a valuable reference for further research on genes related to the body size of animals and their molecular regulatory mechanism.