To obtain a better understanding of how Quaternary climatic oscillations influenced range distributions and intraspecific split of alpine plants on the Qinghai-Tibetan Plateau (QTP) and in adjacent regions, we investigated the extant phylogeographical structure of Bupleurum smithii in this area based on 22 populations and 103 individuals spanning the entire distribution region of this species using chloroplast DNA sequences. Two major haplotype lineages were identified, and at least two corresponding glacial refugia maintaining in the northeastern and eastern edge of the QTP during the Last Glacial Maximum were revealed. Secondary contact between populations and efficient gene flow were also found between two major haplotype lineages. In addition, based on the geographic distribution of haplotypes, we found that populations on the platform derived from individuals that recolonized this area from refugia situated at the northeastern and eastern edges of the QTP, and that B. smithii recolonized from southern to northern China during inter- and post-glacial periods.