It has been suggested that many plants now found in the arctic originated from ancestors that occurred at high altitudes in the southern mountains of the Northern Hemisphere during the Tertiary. However, this hypothesis has rarely been tested using a molecular phylogenetic approach. Here, we present a fossil-calibrated molecular phylogeny of Lagotis, an arctic-alpine genus with the greatest diversity in the Qinghai-Tibetan Plateau (QTP) and Central Asian mountains, based on five chloroplast (matK, psbA-trnH, rps16, trnG-S, trnL-F) and nuclear ribosomal ITS DNA markers. Within this framework, we infer the ancestral area and biogeographic history of the genus. Four major clades (A D) within Lagotis were recovered with strong support, which largely correspond to the previous classification of the genus. Within clade A, Lagotis species from QTP were distributed among several subclades, and L. integrifolia from Central Asia was sister to L. glauca and L. minor from the arctic and subarctic region. The Bayesian molecular dating and the ancestral area reconstruction analyses suggested that Lagotis could have originated in the QTP in the Miocene (Tertiary), and that the genus radiated from the Miocene to Pleistocene. The diversification of Lagotis probably took place predominantly in the QTP and it subsequently spread to the Central Asian highlands, followed by northward migration into the arctic. Our results support the hypothesis that the "Central Asiatic Highland Corridor" as an important route for the migration of the flora between the arctic and QTP.