AimDeserts represent dynamic ecosystems that support communities of endemic and specialised species. We analysed the role of present and past climatic conditions in shaping the distribution of the widespread Bunopus geckos in the Arabian and south‐west Asian deserts. We studied their phylogeographic and demographic history to test whether the Bunopus geckos colonised Arabia from Asia or, vice versa, Asia from Arabia and to identify migration corridors that have historically enabled the dispersal of Bunopus geckos.LocationThe Middle East, especially the Arabian Peninsula.TaxonGenus Bunopus (Squamata; Gekkonidae).MethodsWe generated sequence data for four genes and performed maximum likelihood, Bayesian inference and time‐calibrated phylogenetic analyses and ancestral area reconstruction to infer the phylogenetic and biogeographic history of the genus. We modelled the species' distribution and projected it to several past time periods spanning from mid‐Pliocene to the present. We analysed contemporary landscape connectivity across the peninsula to identify dispersal corridors that enable migration and promote gene flow among Bunopus populations in Arabia.ResultsBunopus is formed by deeply divergent lineages that correspond to up to eight candidate species. The genus originated in southwest Asia and dispersed to Arabia in the late Miocene. The Arabian populations were stable through most of their history in terms of size and distribution extent. Major corridors for contemporary Bunopus dispersal stretch along the eastern Arabian coasts from where they cross through the peninsula to the northern Red Sea coasts.Main ConclusionsThe evolutionary history of Bunopus was substantially influenced by paleoenvironmental conditions. The generalist habits and ground‐dwelling lifestyle enabled the geckos to colonise most of the arid regions of southwest Asia, with Arabia being colonised from the Iranian Plateau in the late Miocene. The distribution extent of Bunopus responded to the past climatic and habitat oscillations; the range was fragmented during moist climatic phases, and it expanded in times of increased aridity. The genus requires taxonomic revision to formally assess its diversity. Based on the results obtained in this study, Crossobamon orientalis is reassigned to Bunopus.