Next generation sequencing yields the complete mitogenome of captive forest musk deer, (Ruminantia: Moschidae).

is an endangered species, but its captive populations are valuable on musk secretions in traditional Chinese medicine and perfume manufacture. The mitogenome of was 16,353 bp in size. Stop codons in 13 PCGs were all typical types except incomplete stop codon T for , and , and TA for No tandem repeat was found in control region. Phylogenetic analysis indicated that Moschidae has the closest relationship with Bovidae. We supported that should be categorized into two subspecies, and suggested that the status of JQ608470 should be further investigated.