Abstract: 【Objective】 In order to find out the differentially expressed genes(DEGs) in the epididymal cauda of yak and cattleyak, functional genes closely related to sperm maturation and storage were excavated, which laid a theoretical foundation for exploring the molecular mechanism of spermatogenesis and maturation process in cattleyak.【Method】 Taking the epididymal cauda of yaks and cattleyaks as the research subject, high-throughput transcriptome sequencing was completed by Illumina 127-HiSeq 2000 platform, and after filtration, quality control and splicing assembly, DEGs were screened out by EBSeq according to the screening criteria of FDR<0.05 and|log₂ Fold Change|>1, and then GO function annotation analysis and KEGG signal pathway enrichment analysis were performed. The accuracy of high-throughput transcriptome sequencing data was verified by real-time fluorescence quantitative PCR.【Result】 A total of 76 DEGs were screened in the caput of the epididymis of yaks and calves, of which 43 DEGs were up-regulated and 33 DEGs were down-regulated. 76 DEGs had annotation information in COG, GO, KEGG, KOG, NR, PFAM, Swiss-Prot and eggNOG databases, especially the highest annotation rate in the COG and Pfam databases(88.16%). The results of GO function annotation analysis showed that DEGs were annotated into three functional categories:biological process, cellular component and molecular function. KEGG signaling pathway enrichment analysis found that 76 DEGs were mainly significantly enriched in 3 signaling pathways, namely bile secretion pathway(ko04976:Bile secretion), ABC transporter (ko02010:ABC transporters) and cAMP signaling pathway(ko04024:cAMP signaling pathway). Eight DEGs(SERPINA1, MMP7, ATP2C1, ABCC1, NMT1, NAT1, CFTR, PRX) were randomly selected for real-time fluorescence quantitative PCR, and the expression patterns of the eight DEGs were basically consistent with the results of high-throughput transcriptome sequencing, indicating that the transcriptome data were accurate and reliable.【Conclusion】 There are 76 DEGs(43 DEGs up-regulated and 33 DEGs down-regulated) in the epididymal cauda of yak and cattleyak, significantly enrich in bile secretion pathway, ABC transporter and cAMP signaling pathway, among which the DEGs associated with sperm capacitation include MMP7, IGFBP2 and ABCC4 genes, the expression of these genes in the epididymal cauda of cattleyak is down-regulated, that is, failure of sperm capacitation may be the main cause of male infertility in cattleyak.