Abstract: Herbaceous plants have a short life cycle and are sensitive to environmental changes. Thus, they may serve as good models to elucidate historical processes of plant populations since Quaternary glaciations. Molecular phylogeographic analysis is a powerful tool to reveal the population history of plants and animals. To understand the geographic history of alpine plants in the Qinghai-Tibet Plateau, which is still poorly known, we surveyed sequence variation of the chloroplast DNA (cpDNA) noncoding fragment trnH (GUG)-psbA intergenic spacer throughout the range of Metagentiana striata (Maxim.) T. N. Ho, S. W. Liu & S. L. Chen, an annual and herba-ceous alpine plant in the Qinghai-Tibet Plateau and adjacent areas. Seven haplotypes were detected by analyzing 155 individuals from 13 populations of this species. One haplotype (A) was common and widespread, and three haplotypes (E, F and G) were unique in their populations. The center of haplotype diversity is located in the Hengduan Mountains of southeastern Qinghai-Tibet Plateau, with 2-3 haplotypes present in each of four popula-tions. In populations from the northeastern and eastern Qinghai-Tibet Plateau as well as from adjacent regions, however, only a single haplotype was found in each population, with different populations having different haplo-types. An analysis of molecular variance (AMOVA) for populations of M. striata showed that the genetic varia-tion mainly resided among populations (73.05%), and the estimates of interpopulation differentiation were very high (GST=0.805, FST=0.731, NST=0.859). Further, a significant phylogeographic structure was present (NST > GST, P<0.05) whereas the value of average gene flow was low (Nm=0.184) in the entire geographical range. Along with the nested clade analysis (NCA), our results suggested that the Hengduan Mountains of southeastern Qing-hai-Tibet Plateau served as a possible refugium during the Quaternary glaciations, and the interglacial or post-glacial range expansion by plants from the refugium followed by allopatric and past fragmentation shaped the present distribution patterns of haplotypes and populations.