Abstract: 【 Objective 】This project aims to screen out genes and pathways related to the double-coated fleece of Hotan sheep in the hope of providing a theoretical basis for further analysis of the molecular regulation mechanism ofdouble-coated fleece of the sheep.【 Methods 】The genome-wide SNPs derived from Hotan sheep with double-coated fleece and Chinese Merino sheep with single-coated fleece were used to determine candidate genes associated with double-coated fleece in Hotan sheep. Healthy adult female Hotan sheep and Chinese Merino sheep were selected with 15 individuals each, blood samples were collected from jugular vein, and genomic DNA was extracted for re-sequencing. Selection signal detection was performed based on whole genome SNPs, and top 1% of Fst and θπRatio value were set as thresholds. SNPs harbored in the strongly selected genomic regions were annotated, then GO function and KEGG pathway enrichment analysis were carried out to further screen out the candidate genes and biologicalpathways related to the double-coated fleece traits of Hotan sheep. 【 Results 】Our results showed that totally 732 selected genes were identified by Fst and θπRatio approaches, and these genes were significantly enriched into several KEGG pathways related to wool traits, even 1 biological process pathway related to hair follicle development.【 Conclusion 】Multiple pathways related to wool traits and five key candidate genes (BMPR2, LPAR6, RARA,CDC6 and BNC1) that may be related to Hotan sheep double-coated fleece were screened.