Past geological and climatic events have promoted intraspecific divergence and range shifts in numerous plant species. This is particularly true for temperate species in climate-sensitive regions. Few previous studies have examined whether such genetic footprints were also shaped in desert plants, which can survive in arid habitats and might be “static” under the past climatic oscillations. We therefore studied the phylogeographical history of Reaumuria soongarica, a shrub species that is widely distributed across the deserts of western China. We sequenced chloroplast DNA (cpDNA) fragments of 27 natural populations across western China. Eight cpDNA haplotypes were identified, which clustered into three clades. The clades were located in the western (clade II) or eastern regions (clades I and III) of western China. Analysis of molecular variance also supported this major partitioning (∼67%) of the cpDNA variation between regions. However, within each region, genetic differentiation was low (29%-37%) and a single dominant haplotype was fixed; this indicated past regional range expansion. The deep divergence and regional range expansions of this species may have corresponded to the most recent uplift of the Qinghai-Tibet Plateau and the development of desert ecosystems during the last glacial age in western China. This is the first study to show that the evolutionary history of plants in desert habitats has been seriously affected by past geological and climatic change.