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Recent studies indicate that hybridization in animals occurs more frequently than previously thought and that it may play an important evolutionary role. Chelonians are capable of extensive hybridization, raising the question how chelonian species evolve and maintain genetic integrity despite hybridization. Here, we use two sister species with parapatric distribution, Mauremys caspica and M. rivulata, as our model. These taxa are estimated to have diverged some 5.3-7.0million years ago. Using rangewide sampling and 13 unlinked polymorphic microsatellite markers, five nuclear loci and one mitochondrial gene, we show that hybridization is rare along the contact zone of the two species in Turkey. However, we discovered an unexpected hybrid swarm in the southern Levant that has been hitherto identified with M.rivulata. This hybrid swarm is separated from the inland species M.caspica by a 700-km-wide distribution gap corresponding to the Syrian Desert. Ecological palaeomodelling suggests that during more humid climatic episodes in the Last Glacial Maximum and mid-Holocene, the current contact zone extended into the southern Levant, facilitating the establishment of the now isolated hybrid swarm. Our results support that there is not necessarily a general hybridization pattern in a given species couple and that the extent of gene flow may differ considerably in different parts of the distribution range. Moreover, our results highlight that studies on hybridization should not focus only on extant contact and hybrid zones, but should use rangewide sampling to detect signals of ancient hybridization that might otherwise be missed.