Abstract To explore the responses of arid-tolerant alpine plants to Pleistocene climatic oscillations, we examined the evolutionary history of Orinus thoroldii, a grass species endemic to the western Qinghai-Tibetan Plateau (QTP) in China. Three maternally inherited chloroplast DNA (cpDNA) markers (matK, rbcL, and trnH-psbA) and the bi-parentally inherited nuclear ribosomal internal transcribed spacer (nrITS) were sequenced for 243 individuals from 28 populations. In all, seven chloroplast haplotypes (H1–H7) and seven nrITS types (S1–S7) were detected. Whereas two haplotypes were widespread, each of the remaining five was restricted to single populations or shared with only its adjacent population. Phylogenetic analyses of the cpDNA haplotypes revealed two distinct lineages distributed in the eastern and western regions of the western QTP. Our analysis of molecular variance (AMOVA) demonstrated the major partitioning (66.56%) of cpDNA variation between the western and eastern groups. A significant phylogeographical structure was detected (NST = 0.81, GST = 0.72; P