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Climate fluctuations of the Quaternary caused radical changes in distribution of tree species and resulted in large-scale range shifts, population contractions and expansions. Scots pine (Pinus sylvestris L.) a widely distributed conifer of the boreal regions underwent spatio-temporal changes, which shaped the modern-day genetic structure and phylogeographic pattern of the species. By applying independent approaches, including molecular genetic data and historical climate models we aimed to describe demography and past distribution patterns of Scots pine populations from the highly fragmented southern periphery, the Carpathians and the Pannonian Basin. We used Approximate Bayesian Computation (ABC) approach based on nuclear microsatellite markers (nSSRs) and Maximum Entropy distribution modelling (MaxEnt) with temperature- and precipitation-related bioclimatic data. ABC results indicated that from an ancestral Scots pine population two genetic lineages have diverged that in the Mid-Pleistocene due to the favourable climatic conditions underwent population expansion leading to an admixture event. The outcome of the hindcasting confirmed the expansion that leaded to the admixture event revealed by the ABC analysis. This can be dated to the Late Glacial period (14,160-11,800 yrs BP), in which widespread distribution of Scots pine in accordance with palynological proxies was detected. Predictions for the Mid-Holocene period have shown large-scale reduction in distribution of Scots pine and low probability of its occurrence, leading to disjunction and population fragmentation. (C) 2017 Elsevier Ltd and INQUA. All rights reserved.