AbstractAimTo examine mechanisms related to the formation of hybrid zones between the Mediterranean narrow‐leaved ash tree Fraxinus angustifolia Vahl and the common ash Fraxinus excelsior L., a mostly temperate tree species, at the continental scale.LocationTemperate and Mediterranean Europe and the western part of the Black Sea basin.MethodsWe used species distribution models to determine the potential zones of sympatry between the two species, which remain largely unknown. In addition, we analysed 58 populations and 456 samples of ash tree that spanned most of the distribution of the two species across Europe, and included both parental species and selected hybrid populations. Levels of hybridization in the 58 populations were estimated using 19 nuclear microsatellite loci, including six anonymous nuclear single sequence repeat (SSR) markers and 13 recently developed single sequence repeats from expressed RNA sequence tags (EST‐SSRs).ResultsBayesian assignment supported the notion of two separate gene pools regardless of the type of marker used, which suggest an ancient population structure. Populations located within the predicted overlap zones had intermediate levels of admixture with a tendency for hybrid populations to occur towards temperate areas. Selection analyses indicated that six of the EST‐SSRs had been subjected to stabilizing selection whereas two others had been subjected to directional selection. Results of spatial filtering on the allele frequencies of the loci under directional selection suggest that the number of days of frost and summer temperatures are both ecological factors that can limit the extent of the hybrid zone. Moreover, areas associated with known or predicted hybrid zones showed abrupt changes in allele frequencies compared with the periphery of the distributions.Main conclusionsOur analyses suggest that the hybrid structure in these closely related ash species is ancient and asymmetric and that climate‐driven selection, in particular cold weather, can potentially limit the extent of hybrid populations.