Abstract: In order to investigate the effects of melatonin on genes expression and to find the functional genes related to hairfollicle development, six five-month-old Inner Mongolia Hanshan Cashmere goats were selected and divided equally andrandomly into two groups, melatonin implantation group （MT） and non-implantation group （CK）. Taking the skin tissue of thegoats as experimental material, RNA-Seq was performed to analyze the transcriptome data by bioinformatics methods. On thebasis of quality control of raw sequencing data, differentially expressed genes （DEGs） were identified, and functional annotationand enrichment analysis were carried out. The results showed that a total of 462 DEGs were screened out, among which, 208 wereup-regulated while 254 were down-regulated. The results of KEGG pathway enrichment analysis elucidated that DEGs aremainly involved in the metabolic pathways, unsaturated fatty acid biosynthesis, fatty acid metabolism, cancer pathways, squamouscell carcinoma pathways, melanogenesis, Wnt signaling pathway and complement and coagulation cascades. Additionally, Wntsignaling pathway may play an important role in melatonin regulation of hair follicle development. This study will provide a basisfor further study on the eftect of melatonin on hair follicle development.