The Anhui musk deer (Moschus anhuiensis) is an endangered species which is endemic to a narrow region in two National Nature Reserves in Dabie Mountains, Anhui Province, China. In this study, we determined the complete mitochondrial genome of M. anhuiensis. The results showed that the total length of the mitogenome was 16,351 bp as a circular DNA and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 control region. Overall base composition of the complete mitochondrial DNA was 34.0% A, 28.1% T, 25.0% C, and 12.9% G. The M. anhuiensis mitochondrial genome had 21 tRNA genes folded in the typical cloverleaf structure, with a unique exception of tRNA(Ser). The mitochondrial genes from M. anhuiensis were overlapped in a total of 72 bp at seven locations, as well as interleaved with a total of 62 bp intergenic spacers.