Various disturbance factors on different spatial scales can lead to the creation of canopy gaps in forest ecosystems. In this study, we investigated the role of root rot fungi in the formation of canopy gaps in the Swiss National Park in the Central Alps. Dying or recently dead mountain pine (Pinus mugo subsp. uncinata trees (n = 172) and saplings (n = 192) from 42 canopy gaps were assessed for Armillaria and Annosum root rot. Heterobasidion annosum s.str. proved to be the dominant pathogen and was isolated from 49% of the trees and 64% of the saplings. Armillaria was found on 13% of the trees and 20% of the saplings. Three Armillaria species, A. borealis, A. cepistipes, and A. ostoyae, were identified. Armillaria ostoyae was the most frequent species, accounting for 72% of all Armillaria isolates. A total of 31 (74%) gaps were associated with H. annosum, and six (14%) with A. ostoyae. The remaining gaps were either associated with both pathogens (7%) or with other, unknown, factors (5%). Our findings suggest that the two pathogenic fungi, H. annosum s.str. and A. ostoyae, are the main reason for the large-scale mortality of mountain pines and the creation of canopy gaps in high elevation forests of the Swiss National Park.