The genetic structure of three newly established Cryphonectria parasitica populations (Choëx, Weggis, Murg) was analysed and compared to an older, post-epidemic population (Claro). Vegetative compatibility (vc) type and DNA fingerprint analysis revealed an almost clonal C. parasitica population in Choëx, Weggis and Murg. These stands are all situated in northern Switzerland, outside the main range of European chestnut. Only one vc type and one dominant DNA fingerprint was found in Choëx and Murg. In Weggis, two vc types and two dominating DNA fingerprints were found. The European Cryphonectria hypovirus (CHV1) was not detected in these three populations. In contrast, the population in Claro, situated within the main range of European chestnut in southern Switzerland, had much higher vc type and DNA fingerprint diversity. DNA fingerprints were correlated to vc types in Claro and in Weggis. Mating type determination revealed one strongly dominating mating type in each of the three northern populations, but not in Claro. From these results we conclude that C. parasitica disseminated almost exclusively by means of asexual reproduction in Choëx, Weggis and Murg, whereas in Claro sexual reproduction also played an important role. Additionally, founder effects and restricted gene flow were dominating factors in shaping the genetic structure of the three northern populations.