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Bark beetle infestation is a widespread phenomenon in temperate forests, which are facing significant weather fluctuations accompanying climate change. Fungi play key roles in forest ecosystems as symbionts of ectomycorrhizal trees, decomposers, or parasites, but the effect of severe disturbances on their communities is largely unknown. The responses of soil fungal communities following bark beetle attack were determined using Illumina sequencing of soil samples from 10 microsites in a mature forest not attacked by bark beetle, a forest attacked by bark beetle, a forest destroyed by bark beetle, and a stand where all trees were removed after a windstorm. The proportion of ITS2 sequences assigned to mycorrhizal fungal species decreased with increased intensity of bark beetle attack (from 70 to 15%), whereas the proportion of saprotrophs increased (from 29 to 77%). Differences in the ectomycorrhizal (ECM) fungal community was further characterized by a decrease in the sequence proportion of Elaphomyces sp. and Russula sp. and an increase in Piloderma sp., Wilcoxina sp., and Thelephora terrestris. Interestingly, the species composition of the ECM fungal community in the forest one year after removing the windstorm-damaged trees was similar to that of the mature forest, despite the sequence proportion attributed to ECM fungi decreased.