Rock Nuthatches comprise two morphologically similar species: Western Rock Nuthatch Sitta neumayer and Eastern Rock Nuthatch Sitta tephronota, with several subspecies within each species. These two species are closely related, and the two together are often considered an offshoot of the Sitta europaea group. The Western Rock Nuthatch is distributed across the Balkans to the Caucasus and Iran while the Eastern Rock Nuthatch is distributed across Eastern Anatolia, Iran, Afghanistan, Turkmenistan and Tajikistan. Using partial mitochondrial ND2 and ND3 gene sequences from populations throughout the distribution ranges and ecological niche modelling, we investigated the genetic structure and biogeographic history of these bird species. Two well-differentiated and supported clades in each species indicated a reciprocal monophyly with no gene flow between birds in the Zagros Mountains and other populations. Ecological niche modelling suggested population contraction in their potential habitat during the Last Glacial Maximum. The genetic differentiation in Zagros Mountains indicates that the post-glacial colonization of most of the Rock Nuthatch distribution range occurred from refugia located elsewhere than the Zagros Mountains. Given that Rock Nuthatches in the Zagros Mountains have long constituted an isolated population, there may be two phylogenetic species within each Rock Nuthatch species. Further genetic studies should be performed for taxonomic clarification.