The genetic diversity and genetic structure of captive forest musk deer (Moschus berezovskii) were investigated using 13 simple sequence repeats (SSR) markers in three core provenances (Bashan, Qinling, and Western Sichuan Plateau). A total of 142 alleles were detected in 167 individuals, and there were 10.92 alleles and 6.373 effective alleles per locus in average. The observed heterozygosity（He）and expected heterozygosity（Ho）were 0.8302 and 0.3897, respectively. The above three populations exhibited relatively high levels of genetic diversity, but still existed the inbreeding phenomenon according to lower observed heterozygosity. It suggested that no significant genetic differentiation existed among populations by the Pairwise Fst and AMOVA analysis. Moreover, these individuals were clustered to three categories by structure analysis (the best K value = 3), which were consistent with their geographical origins, although there were small fractions of introgression among the populations. In conclusion, the Qinling population may be used as a gene pool for idioplasmic improvement due to its high genetic diversity.