Abstract Due to global climate cooling and aridification since the Paleogene, members of the Neogene flora were extirpated from the Northern Hemisphere or were confined to a few refugial areas. For some species, the final reduction/extinction came in the Pleistocene, but some others have survived climatic transformations up to the present. This has occurred in Castanea sativa, a species of high commercial value in Europe and a significant component of the Caucasian forests’ biodiversity. In contrast to the European range, neither the historical biogeography nor the population genetic structure of the species in its isolated Caucasian range has been clarified. Here, based on a survey of 21 natural populations from the Caucasus and a single one from Europe, we provide a likely biogeographic reconstruction and genetic diversity details. By applying Bayesian inference, species distribution modelling and fossil pollen data, we estimated (i) the time of the Caucasian—European divergence during the Middle Pleistocene, (ii) the time of divergence among Caucasian lineages and (iii) outlined the glacial refugia for species. The climate changes related to the Early–Middle Pleistocene Transition are proposed as the major drivers of the intraspecific divergence and European–Caucasian disjunction for the species, while the impact of the last glacial cycle was of marginal importance.