The fungus Ophiocordyceps sinensis is endemic to the vast region of the Qinghai-Tibetan plateau (QTP). The unique and complex geographical environmental conditions have led to thesky islanddistribution structure of O. sinensis. Due to limited and unbalanced sample collections, the previous data on O. sinensis regarding its genetic diversity and spatial structure have been deemed insufficient. In this study, we analyzed the diversity and phy-logeographic structures of O. sinensis using intally transcribed spacer region (ITS) and 5-locus datasets by a large-scale sampling. A total of 111 haplotypes of ITS sequences were identified from 948 samples data of the fungus O. sinensis, with representing high genetic diversity, and 8 phylogenetic clades were recognized in O. sinensis. Both the southeast Tibet and the northwest Yunnan were the centers of genetic diversity and genetic differentiation of the fungus, and they were inferred as the glacial refugia in the Quatary. Three distribution patts were identified to correspond to the 8 clades, including but not limited to the coexistence of widely and specific local distributive structures. It also revealed that the differentiation patt of O. sinensis did not fit for the isolation-by-distance model. The differentiation into the 8 clades occurred between 1.56 Myr and 6.62 Myr. The ancestor of O. sinensis most likely originated in the late Miocene (6.62 Myr) in the northwest Yunnan, and the Scene A–C of the Qinghai–Tibetan movements may have played an important role in the dif-ferentiation of O. sinensis during the late Miocene–Pliocene periods. Our current results provide a much clearer and detailed understanding of the genetic diversity and geographical spatial distribution of the endemic alpine fungus O. sinensis. It also revealed that the geochronology resulting from paleogeology could be cross-examined with biomolecular clock at a finer scale.