East Asia harbors the highest level of floristic diversity among the world's temperate regions. Despite the increase in phylogeographic studies of temperate plants in East Asia, far less attention has been paid to widely distributed deciduous shrubs that widespread across several floral regions. We sequenced two chloroplast DNA (cpDNA) fragments (ndhJ-trnF and trnD-trnT) and one nuclear DNA (Pgk1) of 472 individuals from 51 populations of such a group, the Indigofera bungeana complex. We used population genetic data as well as ecological niche modelling to examine the evolutionary history and glacial refugia during the Last Glacial Maximum (LGM) of this group. We recovered 133 cpDNA and 68 nuclear haplotypes. The star-phylogeny of the recovered cpDNA and nuclear haplotypes and demographic analyses suggested distinct range expansion of I. bungeana complex have occurred during the early and middle Pleistocene. The climate change of the LGM might have affected little on the distribution of this complex based on the niche modelling. However, these climate changes and geographic isolation probably resulted in fixtures of the private haplotypes and genetic differentiations between regions. Our results suggested that this arid-tolerant species complex may have different responses to the Quaternary climate changes with those climate-sensitive species.