In this paper, we sequenced the complete mitochondrial genome of the Manis pentadactyla (Pholidota: Manidae), which is considered as an endemic species in China. It is listed as a vulnerable species by the International Union for Conservation of Nature and Natural Resources Red List and also an endangered species in China. The genome is 16,578 bp in size. Its gene arrangement pattern was identical with those of Manis tetradactyla. We compared the mitochondrial genome of M. pentadactyla with that of the M. tetradactyla. Nucleotide sequence similarity between the two whole mitochondrial genomes was 79.30%, and the relatively low similarity seems to indicate that the two species are distinctly separated on the species level. The information on the mitochondrial genome comparison of the two species was discussed in detail in this paper.