Simple SummaryForest musk deer (Moschus berezovskii) is a species that is currently classified as endangered and found in China and Vietnam. In order to prevent their extinction, China initiated captive breeding programs in the 1950s. Maintaining the high genetic diversity of the population is a crucial factor for ensuring the sustainable and rapid growth of these captive populations. Mitochondrial DNA (mtDNA) possesses a unique lineage of matrilineal evolution, and the control region (CR) is considered to be one of the most popular molecular markers for conducting a genetic diversity analysis and determining maternal lines. In this study, we assessed the current genetic diversity status of 338 individuals from seven captive forest musk deer populations located in the Shaanxi province using mtDNA CR, and the results showed that the genetic diversity was high. We also made full use of previous mtDNA CR data clearly defining 65 haplotypes with their frequency and concluded with about 90 maternal lines. The analysis revealed no significant genetic differentiation among the populations, and the populations might not have experienced rapid population expansion. The current study represents the most comprehensive research of genetic diversity of captive forest musk deer to date, and will be helpful to preserve and enhance the genetic diversity of the captive forest musk deer populations.AbstractForest musk deer (Moschus berezovskii) are endangered ruminants whose adult males secrete musk. China has been breeding forest musk deer artificially since the 1950s in an effort to restore wild populations, with Shaanxi and Sichuan provinces as the two main sites for captive breeding. Genetic diversity is a significant indicator that determines the long-term viability and status of a population, particularly for species at risk of extinction. In this study, we analyzed the current genetic makeup of seven captive forest musk deer populations in the Shaanxi province, using the mitochondrial DNA (mtDNA) control region (CR) as the molecular marker. We sequenced 604 bp of mtDNA CR, with an average content of A+T higher than G+C. We observed 111 variable sites and 39 different haplotypes from 338 sequences. The nucleotide diversity (Pi) and haplotype diversity (Hd) were 0.02887 and 0.908, respectively. Genetic differentiation between these populations was not significant, and the populations might not have experienced rapid growth. By combining our sequences with previous ones, we identified 65 unique haplotypes with 26 rare haplotypes and estimated a total of 90 haplotypes in Shaanxi province captive populations. The Shaanxi province and Sichuan province obtained 88 haplotypes, the haplotypes from the two populations were mixed together, and the two populations showed moderate genetic differentiation. Our findings suggested that captive forest musk deer populations in the Shaanxi province had high genetic diversity, with a rich founder population of about 90 maternal lines. Additionally, managers could develop genetic management plans for forest musk deer based on the haplotype database. Overall, our study will provide insights and guidelines for the conservation of genetic diversity in captive forest musk deer populations in the Shaanxi province.