The phylogeographical structure of hoary bamboo rat (Rhizomys pruinosus) was studied based on the mitochondrial cytochrome b gene sequences of 160 individuals from 37 populations over most ranges on Yunnan Guizhou Plateau.A total of 76 haplotypes identified clustered into four geographically clades in this studied area.The results from molecular variance analyses showed that restricted gene flow and genetic variation were significantly occurred between four diverged geographical clades in phylogenetic trees.Nested clade analyses revealing significant associations between genetic structure and geographical division identify past fragmentation and restricted gene flow as major phylogeographical events that shaped the geographic distribution of this species in Yunnan-Guizhou Plateau, coupled with population recolonization or expanding were not be found in these four diverged groups.Coalescent tests supported the hypothesis that there was at least one refugium covered the Hengduan mountain during the Last Glacial Maximum.The genetic diversity analyses showed that the diversity indices of the four diverged clades did not vary significantly, but they were much lower than those of other subterranean rodent of plateau zokor endemic to Qinghai Tibetan plateau.Therefore, our results suggest that the Pleistocene glaciations, geologic diastrophisms and human activity induced the intraspecific genetic variation of the R.pruinosus into geographical elades.These findings could provide basic information for the future studies in animal ecology, comparative phylogeography and genetics, as well as an important reference for the evaluation, conservation, and utilization of the genetic resources of this species.