Taxus wallichiana var.mairei (Lemée & Léveillé) L.K.Fu & Nan Li is a highly endangered conifer,a total of six haplotypes were detected in all 499 individuals of 18 populations,in chloroplast DNA trnL-F fragment by PCR-RFLP.H1 and H2 existed in all the populations distributing in mainland of China,but H3 only existed in Huangshan population,and H4 only existed in Lin’an population,with H5 and H6 coexisting in Taiwan population.The phylogeographic analysis suggested the H1 and H2 were the ancestor haplotypes,while the other haplotypes were evolved from them.Some 26.39% of the total variation existed among the populations,while 73.61% in the populations suggested by AMOVA.NCA analysis suggested there was slight correlation between the distribution of cpDNA haplotypes and geography,and the genetic structure of T.wallichiana var.mairei resulted from the effect of population fragment or the long-distance colonisation.Variation of cpDNA haplotypes suggested several glacial refugiums of T.wallichiana var.mairei in the east and south of China.