Objective  The research aimed to study the genetic diversity and genetic structure of the captive forest musk deer population, and provide scientific basis for guiding the population genetic management and protection and utilization of breeding population germplasm.

  Method  This study collected 220 fresh samples from Pianzaihuang Musk Deer Farm and Fengchun Musk Deer Farm in Feng County, Baoji City, and Taiziling Musk Deer Farm in Liuba County, Han Zhong City of Shaanxi Province, northwestern China and sequenced 112 mitochondrial DNA control region sequences successfully. Haplotype diversity and nucleotide diversity were calculated.

  Result  The 96 mutation sites were detected in the three forest musk deer breeding farms, all of which were simple information sites, with the mutation forms of conversion and translocation, without insertion or deletion. A total of 36 haplotypes were obtained, and the haplotype diversity and nucleotide diversity were 0.957 8 and 0.039 5, respectively. The haplotype diversity was the highest in Pianzaihuang population (0.953 9) and the lowest in Liuba population (0.842 8). The three populations showed significant genetic differentiation, among which the genetic differentiation coefficient F_ST (0.137 7) of Taiziling musk deer population and Fengchun musk deer population was the highest, while the F_ST (0.077 2) between Pianzaihuang and Taiziling was the lowest.

  Conclusion  The genetic diversity of the captive forest musk deer is higher than that of many endangered ungulate species in captive, but the gene exchange among their breeding population is limited, and genetic differentiation has appeared. It is suggested to strengthen the exchange of genetic sources and enhance the gene exchange in order to help protect the genetic diversity of forest musk deer populations in captive.