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Quaternary climatic oscillations appear to have influenced the genetic diversity and evolutionary history of arid-adapted plants. To understand the processes involved and reveal evolutionary relationships, haplotypes were examined from Calligonum roborovskii, an endemic species occurring in the arid zones across the desert regions of north-western China, and seven other species also from Calligonum section Medusa, including C.gobicum, C.mongolicum and the narrow endemic species C.ebi-nuricum, C.pumilum, C.taklimakanense, C.trifarium and C.yengisaricum. Forty-three haplotypes were identified in 422 individuals from 51 natural populations, from variation of two plastid DNA intergenic spacers (rpl32-trnL and ycf6-psbM). A high level of total genetic diversity was found across species for which more than two populations were examined, including C.gobicum, C.mongolicum, C.pumilum and C.roborovskii. A distinct isolation-by-distance pattern in each of these species was suggested by the Mantel test, indicating that restricted gene flow caused high genetic differentiation among populations. Three haplotypes were shared by two or three species each, but the other 40 haplotypes were species-specific. The 43 haplotypes split into three major clades, but not species-specific lineages; most of the Calligonum species were not reciprocally monophyletic, probably due to incomplete lineage sorting or introgression. The identified haplotypes were dated to 1.97Mya (95% highest posterior density: 2.95-0.99Mya) and diverged until the late Pleistocene, possibly linked to aridification and enlargement of deserts caused by climate changes. Variation of desert habitats during the Pleistocene might play a key role in causing the divergence.