Objective To analyze the genetic diversity and phylogenetic of Macaca mulatta in Yunnan Province, which provide important reference and background data for researches of macaca mulatta protection and reasonable application. MethodsNinety six blood samples of Macaca mulatta were collected for amplifying the complete sequences of mitochondrial DNA control region by polymerase chain reaction (PCR). The variation sites, parsimony informative sites, haplotypes, haplotype diversity, and nucleotide diversity were analyzed using Mega 4.0 and DNA SP software. The phylogenetic tree was constructed by neighbor-joining (NJ) and minimum-evolution(ME) methods.ResultsOne hundred and forty-nine variation sites and 46 haplotypes were found in the ninety-sixth Macaca mulatta, the haplotype diversity (Hd) was 0.968±0.007 and nucleotide diversity (Pi) was 0.020. The phylogenetic analysis based on mitochondrial control region showed that these Macaca mulatta lived in Yunnan was divided into two sister groups geographically. ConclusionsThe results of this study indicate a high variation and phylogenetic evolution relationship of Macaca mulatta in Yunnan province. 