To extend our knowledge of population structure of Cryphonectria parasitica in the Aegean region, 264 isolates obtained from eight subpopulations in Izmir, Manisa and Denizli provinces were studied. Only three vegetative compatibility (vc) types, EU‐1, EU‐12 and EU‐2, were identified. EU‐1 (59%) was dominant and was found in all eight subpopulations. EU‐12 (32%) was detected in six subpopulations and was highly dominant (71%) in the Ödemiş subpopulation (İzmir province). EU‐2 was restricted to only one subpopulation, Tire, but, there, had the highest frequency (50%). This is the first reported occurrence of EU‐2 in western Turkey. Regarding sexual compatibility, both MAT1‐1 and MAT1‐2 were detected in all subpopulations; however, 85% of the isolates were MAT1‐1 and no perithecia were found in any of the subpopulations. Multilocus linkage disequilibrium analysis determined that all subpopulations were clonal. Indicator co‐kriging representations showed that vc types and mating types were spatially aggregated. In combination, these results indicate that the dispersal of the pathogen most likely occurs via localized short‐distance transport of rain‐splashed asexual conidia, rather than the long‐distance dispersal of wind‐borne ascospores. Because of the presence four polymorphic vegetative incompatibility (vic) loci in certain subpopulations, C. parasitica has the potential to generate new vc types in the future.