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Cynips quercusfolii is an oak gall wasp species distributed across the western Palearctic region. In this study, C. quercusfolii adults were used to investigate the possible effects of past climatic fluctuations and topography on the genetic structure of this species in Turkey. For this, the partial mitochondrial DNA (mtDNA) cytochrome b gene (cyt b) and nuclear DNA (nDNA) ITS2 region of 294 individuals from 38 populations covering the distribution of this species in Turkey were sequenced. The sequences generated 125 mtDNA haplotypes and 30 nDNA alleles. High variation was revealed in Turkish populations of C. quercusfolii (h = 0.7328 and pi = 0.0102 for cyt b, and h = 0.5865 and pi = 0.0058 for ITS2). Demographic analyses and high haplotype versus low nucleotide diversity indicated that C. quercusfolii populations might have undergone a series of expansions and contractions in the past. Phylogenetic analyses showed that this species is structured geographically between east and west due to a major physical barrier, the Anatolian Diagonal. Furthermore, divergence times of the lineages implied that deep splits occurred before the Pleistocene, while intermediate to shallow splits were associated with climatic changes during the Pleistocene. We conclude that ongoing geological events and associated climatic cycles were responsible for the current population genetic structure of this species in Turkey.