Simple SummaryPrevious paleoclimatic modelling studies on the European whip snake,Hierophis viridiflavus, hardly explain its genetic structure. Through the combination of phylogeographic and paleoclimatic modelling analyses, we reconstructed the biogeographic history of the species. Phylogeographic analyses recovered two major lineages that had diversified in different ways in the late Pleistocene. Paleoclimatic models unveiled the species range dynamics since the late Pleistocene, showing major range contractions into multiple climatic refugia in Southern Europe during glacial and interglacial events, as well as more recent northwards expansions. This study contributes to our knowledge ofH. viridiflavus’historical biogeography and sheds more light on the evolutionary processes that took place in the Mediterranean Basin hotspot.AbstractPhylogeographic and paleoclimatic modelling studies have been combined to infer the role of Pleistocene climatic oscillations as drivers of the genetic structure and distribution of Mediterranean taxa. For the European whip snake,Hierophis viridiflavus, previous studies based on paleoclimatic modelling have depicted a low reliability in the pattern of past climatic suitability across the central Mediterranean Basin, which barely fits the species’ genetic structure. In this study, we combined phylogeographic and paleoclimatic modelling tools to improve our understanding of the biogeographic history ofH. viridiflavus, particularly extending the sampling and phylogeographic inferences to previously under-sampled regions. Phylogeographic analyses recovered two major clades that diverged at the beginning of the Pleistocene and had diversified in different ways by the late Pleistocene: the east clade (composed of three subclades) and the west clade (with no further structure). Paleoclimatic models highlighted the temperate character ofH. viridiflavus, indicating range contractions during both the last inter-glacial and last glacial maximum periods. Range expansions from southern-located climatic refugia likely occurred in the Bølling–Allerød and Middle Holocene periods, which are supported by signals of demographic growth in the west clade and South–East–North subclade. Overall, this work improves our understanding of the historical biogeography ofH. viridiflavus, providing further insights into the evolutionary processes that occurred in the Mediterranean Basin hotspot.