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We conducted a comparative phylogeographic analysis of three rodent species (Meriones meridianus, Dipus sagitta, and Allactaga sibirica) on the northeast margin of the Qinghai-Tibetan Plateau, Qaidam Basin, the Hexi Corridor and Tengger-Badain Jaran Desert based on sequences of the mitochondrial cytochrome b gene of 264 individuals from 22 sampling sites. Our analyses indicated that the intraspecific genetic structures of the three rodents did not arise through the same historical events and that they did not show parallel geological and climatic histories. M. meridianus and D. sagitta, which showed low-altitude distributions, experienced less isolation because they stayed in stable favorable habitats. On the other hand, A. sibirica was strongly isolated due to fragmented habitats caused by the complex topography of the high-altitude regions in the Qaidam Basin. The two desert-dwelling rodent species, M. meridianus (0.023-0.014 Mya) and D. sagitta (0.013-0.009 Mya), showed sudden demographic expansion during the Last Glacial Maximum, with the disappearance of the ancient lakes and the maximum extent of desert expansion. A. sibirica is mostly distributed in the grassland mountain regions. Thus, steppe expansion and a sharp decrease in the ancient lake size significantly affected the species’ distribution during the Middle Pleistocene (0.525 Mya). No clear signal of population expansion was observed for this species, which might be attributable to successive phases of population bottlenecks obscuring the indicators of expansion. Our data reflect the continual interaction of extrinsic and intrinsic factors in generating intraspecific phylogeographic patterns and faunal diversity. (C) 2015 Deutsche Gesellschaft fur Saugetierkunde. Published by Elsevier GmbH. All rights reserved.