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鄄bp fragment of the mitochondrial DNA (mtDNA) D鄄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鄄loop region. A total of 171 variable