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The dwarf musk deer, or Chinese forest musk deer (Moschus berezovskii) is an endangered artiodactyl species native to a narrow region in southern and central China as well as northernmost Vietnam. This species is well known for the habit of male musk deer to secrete musk from the musk gland. Unmated male forest musk deer secrete a greater amount of musk than mated males, which probably allows them to attract a greater number of females. However, transcriptome data for this species are deficient, and the potential transcriptional pathways of musk production remain unknown. In this study, we used RNA-sequencing (RNA-Seq) to perform an in-depth survey of transcriptome data from musk gland and to compare the transcriptome differences between mated- and unmated sexually mature Chinese forest musk deer. There were 13,009 and 12,995 genes were expressed in unmated and mated musk glands tissue. In addition to analyzing these genes, we analyzed the differentially expressed genes in musk gland tissue between mated and unmated Chinese forest musk deer males. One hundred and thirty seven genes were found differentially expressed. We found that some genes in “PPAR signaling pathway”, “PI3K-Akt signaling pathway” and “Thyroid hormone synthesis” pathways may be associated with musk production and the secretion of the musk deer. The annotated genes and differentially expressed genes in this study can be applied in conservation or utilization study of musk deer in the future.