Forest musk deer (Moschus berezovskii) were once distributed widely in China. However, wild populations in the Qinling Mountains have declined dramatically because of poaching and habitat loss. Captive breeding populations have been established for several decades, but the genetic background of most captive populations has been unclear and the populations have increased very slowly. In order to gather useful information for the conservation and management of this species, we investigated the genetic diversity and population structure of forest musk deer by analyzing a 632-bp fragment of the mitochondrial DNA (mtDNA) D-loop region in one captive breeding population and three wild populations in Shaanxi Province, China. The captive breeding population was from the Fengxian musk deer plant; the three wild populations were from Fengxian, Liuba and Longxian Counties. The mtDNA was extracted from two samples: hair and muscle. The average contents of A+T (63.2%) were higher than those of G+C (36.8%) in the mtDNA D-loop region. A total of 171 variable sites (about 27.05% of the total nucleotides in the sequence) were detected in 69 individuals. The nucleotide diversity (Pi) of the 69 individuals was 0.04424, and the average number of nucleotide differences (K) between them was 19.908. The 69 individuals belonged to 32 haplotypes, according to the determined sequences. The average genetic distance (P) among the haplotypes of the species was 0.070. Analysis of the phylogenetic tree using the neighbour-joining method showed that the 32 haplotypes were clustered into three groups. The 32 haplotypes were randomly distributed between the four forest musk deer populations. By means of the median-joining method, we found that haplotype 3 was located in the center of the star graph, and that the other haplotypes were associated with haplotype 3 by 1-38 steps. The average genetic distance of the four groups was 0.0434 (standard error 0.005). The genetic relationship between the Fengxian musk deer plant and Liuba populations was distant. The average genetic distance among the haplotypes was 0.043, so the genetic differentiation had not yet reached the level of population differentiation. Our data indicated that the variation and genetic diversity were high in the four populations of Moschus berezovskii. The captive breeding population and the wild population in Fengxian both had a higher nucleotide diversity and haplotype diversity. There was no inbreeding or genetic diversity reduction in the captive breeding population. The analysis of molecular variance demonstrated that most variation occurred within samples and that there was significant differentiation between the four populations. The genetic differentiation between the farm populations and the wild populations in Fengxian was small, with a high degree of gene flow. Estimates of the gene flow indicated that there were few genetic exchanges among the four populations. Building pedigree records and increasing the gene flow between populations will help to conserve these populations and this species.