Asaccus geckos are distributed in southwest Asia, mainly in Iran and Arabia. Currently, seven Asaccus species are recognized in Arabia, all endemic to the isolated Hajar Mountains in Oman and the UAE, an area regarded as a biodiversity and endemicity hotspot. Previous phylogenetic studies have shown a non‐monophyletic structure of the Arabian Asaccus species, with the Hajar endemic A. montanus diverging first from the remaining Iranian and Arabian taxa, thus suggesting a possible Arabian origin for the genus. Despite the species’ obvious phylogeographical importance, no study has yet explored its intraspecific diversity. In this study, we assessed the genetic diversity and phylogeography of A. montanus and its phylogenetic relationships with the rest of the Arabian Asaccus species and some available representatives from Iran. We used both mitochondrial and nuclear data to assess phylogenetic relationships based on haplotype networks, concatenated datasets and species trees, performed species delimitation analyses, and estimated divergence times and genetic diversity. We suggest Asaccus began diverging during the Middle Oligocene, a period of major tectonic activity in and around Arabia. Our results mainly support previous phylogenetic studies and uncover the presence of cryptic diversity within A. montanus. Asaccus montanus diverged in the Jebel Akhdar Mountain range into two deep allopatric lineages during the Late Pliocene. Our findings suggest further taxonomic research is necessary for this species, especially due to its vulnerable status and restricted range in an area of great conservation importance.
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