Armillaria species are plant pathogens that cause Armillaria root rot and are known to cause mortality of mountain pines (Pinus mugo) in the Swiss National Park in the Central Alps. The identity of isolates and the spatially explicit population structure of the Armillaria species were investigated in a 3.3 km² study area in the Swiss National Park. In total, 242 Armillaria isolates, 205 from wood samples and 37 from epiphytic rhizomorphs, were collected. Species were identified using haploid-diploid pairings and genets were determined using intraspecific somatic incompatibility tests. The population structure differed markedly among the Armillaria species. A. cepistipes and A. borealis mainly occurred as genets of small spatial extent (mean 0.2 ha, and 0.6 ha), whereas A. ostoyae formed significantly larger genets (mean 6.8 ha). The largest A. ostoyae genet extended over approx. 37 ha. Several disease centres associated with Heterobasidion annosum were found to be embedded within large Armillaria genets. The extension of large A. ostoyae genets suggests that forests that occupy the study area have developed in the presence of these Armillaria genets. The finding of large Armillaria genets supports the assumption that large genets occur in areas with cold climate and little precipitation.