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Tibetan macaque (Macaca thibetana) is a threatened primate species endemic to China.Population genetic and phylogenetic analysis were conducted in 66 Tibetan individuals from Sichuan (SC),Huangshan (HS) and Fujian (FJ) based on a 477-bp fragment of mitochondrial DNA control region.Four new haplotypes were defined and a relatively high level of genetic diversity was first observed in FJ populations (Hd = 0.7661).Significant genetic differentiation had occurred among three populations (FST = 0.8700),especially a continuous aproximately 10 bp-fragment deletion was observed near the 5'end of the mtDNA control region of HS and FJ populations when compared with that of SC population,but genetic differentiation between HS and FJ populations belonging to M.thibetana huangshanensis and M.thibetana pullus,respectively,did not reach the level of subspecies division yet,and hence not support traditional morphological taxonomy.we propose to retain the name of M.thibetana pullus,and remove M.thibetana huangshanensis.