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Hog deer (Axis porcinus) is a small mammal and listed in the International Union for Conservation of Nature. However, phylogenetic position of hog deer within Axis genus has remained controversial. In the present study, we first assembled complete mitochondrial genome of Chinese hog deer reared in Chengdu Zoo, Sichuan, by the second-generation sequencing technology. This newly assembled mitochondrial genome of hog deer is 16 376 bp in length and consists of 13 protein-encoding genes, 23 transfer RNA genes and 2 ribosomal RNA genes. Phylogenetic analyses based on complete mitochondrial genome and cytochrome b gene sequences revealed that hog deer is closely clustered together and placed with sister taxon of spotted deer (A. Axis), which therefore supported monophyletic statue of Axis genus. Furthermore, considerable genetic differentiation, up to 139 mutations of complete mitochondrial genome was revealed between geographical populations of hog deer in France and Southeast Asia. However, only six variable sites (nucleotide diversity of 0. 000 07) and four haplotypes (haplotype diversity of 0.533) were totally detected among ten newly sequenced Chinese hog deer. The results provide a better understanding on the phylogeny of hog deer. [ABSTRACT FROM AUTHOR]