Cynips quercus is a with widespread oak-gall wasp species distributed across the Western Palearctic from Europe, the northern Caucasus and North Africa to Iran. In this study, we used 175 asexual-generation individuals of C. quercus collected from 30 localities in Turkey to investigate the effects of topography and climatic factors on the phylogeographic structure of the species. Sequence analysis of the mitochondrial cytochrome-b gene (MT-CYB) and the nuclear ITS2 region supported a genetic break between the eastern and the western sides of the Anatolian Diagonal. The ITS2 results indicated that the populations underwent expansion, while in contrast the MT-CYB data implied a stable population structure for C. quercus. Molecular clock applied to the MT-CYB data suggested that the climatic and environmental changes during the Pliocene and Pleistocene had a profound effect on the phylogeography of the species.