[Objectives] Forest Musk Deer Moschus berezovskii is first class protection wildlife in China. In order to protect the wild Forest Musk Deer population and meet the demand for natural musk in traditional Chinese medicine and other industries, China began to raise Forest Musk Deer artificially in the 1950s. Maintaining high genetic diversity of the population is the key factor to realize the sustainable growth and release of the captive Forest Musk Deer population into the wild. [Methods] In Fengxian County, Shaanxi Province, we collected feces samples from 95 Forest Musk Deer in two captive populations and kept all the samples in a lab refrigerator at﹣20 ℃ until DNA extraction. We selected published tetranucleotide microsatellite loci, then identified microsatellite loci that can be reliably amplified from fecal DNA. The forward primers of these loci were colored with fluorescent dyes and used to analyze the genetic diversity of 95 captive Forest Musk Deer. [Results] Twenty-five tetranucleotide microsatellite loci of Forest Musk Deer were obtained, of which 21 could be steadily amplified from fecal DNA, and two of them had chaotic peaks that were not suitable for analysis (Appendix 1). For the 19 microsatellite loci, there were 7 loci with polymorphism information content > 0.5, which were high polymorphism loci, and 10 loci were consistent with Hardy-Weinberg equilibrium (P > 0.05) (Table 1). Among the two populations studied, 95 individuals had 99 alleles and 43.880 5 effective alleles, the mean of Shannon’s index and polymorphism richness were 0.930 6 and 0.428 3 respectively. The mean observed heterozygosity was 0.449 4, and the mean expected heterozygosity was 0.467 5. The genetic diversity of the Fumin farm population was higher than that of the Haixing farm (Table 3). All the Forest Musk Deer individuals came from four gene clusters. The Forest Musk Deer of the Fumin farm mainly came from gene cluster 1 and 2, and the Forest Musk Deer of the Haixing farm mainly came from gene cluster 3 and 4 (Fig. 2). [Conclusion] The selected microsatellite loci were 13 more than the previous studies, which can provide a reference for future studies on genetic diversity of Forest Musk Deer based on fecal samples. The captive Forest Musk Deer in Fengxian County, Shaanxi Province showed high genetic diversity but a tendency to inbreed. The genetic differentiation of Fumin Forest Musk Deer farm and Haixing Forest Musk Deer farm was small, and there was a large gene flow. It is suggested that the provenance of each captive population can be changed to increase the degree of heterozygosity.