Studies on the influence of Pleistocene climatic fluctuations and associated habitat changes on arid-adapted bird species living in the Holarctic region are comparatively rare. In contrast to temperate species, the populations of arid-adapted avian species might be characterized by low genetic differentiation because periods of population isolation were associated with the short interglacial periods, while population expansion events might have occurred during the longer glacial periods when steppe-like vegetation might have been prevalent. In this study, we tested this hypothesis in a widespread arid-adapted taxon of the Palaearctic desert belt, the Houbara–Macqueen's bustard complex. The later includes the Houbara bustard Chlamydotis undulata, comprising the North African subspecies Chlamydotis u. undulata and Chlamydotis u. fuertaventurae from the Canary Islands, and the Asian Macqueen's bustard Chlamydotis macqueenii. A long fragment (1042 bp) of the Cyt-b gene was investigated in 39 representatives of the two species to assess phylogenetic and phylogeographic patterns, and demographic history and to compute divergence time estimates using a Bayesian relaxed molecular clock approach based on different coalescent priors. While the two species are genetically distinct, we found little intraspecific genetic differentiation. The divergence time of the two species falls within a period of extreme aridity at around 0.9 million years ago, which most likely resulted in an east–west vicariance along the Arabo-Saharan deserts. Differentiation within Houbara and Macqueen's bustard occurred later during the Middle to Upper Pleistocene, and as we have predicted, periods of range expansion were associated to the last glacial period at least in the Macqueen's bustard.