• Premise of the study: Large‐scale studies on the genetic diversity of forest trees are relevant for the inventory, conservation, and management of genetic resources and provide an insight into the geographical origins of the species. This approach is appropriate to use with Castanea sativa, a tree of great economic importance and the only species from the genus Castanea in Europe. The history of C. sativa was deduced from fossil pollen data, but the large‐scale genetic structure of this species needs to be elucidated. We evaluated the genetic diversity of C. sativa to define previously unclarified genetic relationships among the populations from Turkey and those from Greece and western Europe. The influence of natural events such as glaciations and human impact in terms of species distribution are discussed.• Methods: Wild chestnut trees (779) were sampled in 31 European sites. Six polymorphic microsatellites were used for the analysis. A set of measures of intra‐ and interpopulation genetic statistics were calculated. The population structure was inferred by using a Bayesian approach.• Key results: The population structure showed a genetic divergence between the eastern (Greek and Turkish) and western (Italian and Spanish) populations. Two gene pools and a zone of gene introgression in Turkey were revealed.• Conclusions: The inferred population structure shows a strong geographical correspondence with the hypothesized glacial refugia and rules out the migration of the chestnut from Turkey and Greece to Italy. The homogeneous gene pool observed in Italy and Spain could have been originated from common refugia along with human‐mediated colonization.