•In its natural distribution area Turkish hazel has been overexploited because of its valuable wood and can only be found in small and isolated populations.•Therefore, we examined the genetic structure and variation of Turkish hazel covering most of its natural distribution area in Asia Minor, the Caucasus, and the Balkan Peninsula.•Altogether, 689 Turkish hazel trees from 25 populations based on 15 nuclear and five chloroplast microsatellite markers were studied.•Both data sets revealed distinct genetic structures of Turkish hazel in its natural distribution range, suggesting separate refugia and migration pathways during the Holocene.•Medium to high level genetic variation was found, with somewhat lower values in Georgia and Turkey compared to the Balkan populations.•Overall, our results highlight needs to delineate provenance regions, identify conservation units and seed stands for Turkish hazel which are essential for species conservation, provenance research and possible assisted migration attempts.•Based on our results each country is able now to start the conservation programs and select GCUs for Turkish hazel. Climate change is already affecting all forest ecosystems and threatening species therein. By establishing mixed forests incorporating other tree species (e. g. scattered broadleaves) adaptation of forest stands to changing environmental conditions can be improved and the risks minimized. Turkish hazel (Corylus colurna L.) has been currently discussed as a valuable so-called alternative tree species in some European regions because it is well adapted to difficult environmental conditions. However, in its natural distribution area Turkish hazel has been overexploited because of its valuable wood and can only be found in small and isolated populations. Therefore, we examined the genetic structure and variation of Turkish hazel covering most of its natural distribution range in Asia Minor, the Caucasus, and the Balkan Peninsula. Altogether, 689 Turkish hazel trees from 25 populations were analysed at 15 nuclear and five chloroplast microsatellite markers. Both data sets revealed distinct genetic clusters of Turkish hazel in its natural distribution range, suggesting separate refugia and migration pathways during the Holocene. Medium to high level genetic variation was found, with somewhat lower values in Georgia and Turkey compared to the Balkan populations. Overall, our results highlight the need to delineate provenance regions, identify gene conservation units (GCUs) and seed stands for Turkish hazel which are essential for species conservation, provenance research and possible assisted migration attempts. Based on our results each country is able now to start conservation programs and select GCUs for Turkish hazel.