Project description:White-cheeked macaque is a newly described species in genus Macaca. Here, the complete mitochondrial genome was firstly determined, which was deposited in Genbank with accession number KU564271. The length of the mitogenome is 16,494 base pairs (bp). It includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes and a control region. We used 12 mitochondrion genes of 15 species to constructed phylogenetic tree with three methods. The study will provide useful data for further studies on phylogenetic relationships as well as population structure, biodiversity conservation and conservation genetics.