We studied the changes in the wood-inhabiting fungal communities on dead wood of Scots pine ( Pinus sylvestris ) under varying duration and intensity of cormorant nesting. The activities of the birds created large amounts of dead wood, changed wood chemistry and altered stand characteristics. Analyses based on records of fruiting structures of fungi showed that fungal communities in the cormorant colony differed from communities in unaffected forest. Ornithogenic factors impacted least on generalist species and promoted the occurrence of fungi uncharacteristic of coniferous wood or wood in general. The rate of ornithogenic change was rapid: a shift in fungal assemblages was evident by the third year of expansion of the bird colony into unaffected forest. It featured the disappearance of tremelloid fungi, a decline of corticioid fungi and an increase of hyphomycetoid fungi. The proportion of coniferous wood specialists decreased and that of generalists increased. It is expected that the changes in fungal communities will persist until the forest is fully regenerated. • The impact of cormorant nesting on wood-inhabiting fungal communities was studied. • Fungal communities under bird impact differed from those in unaffected forest. • Fungi not normally associated with coniferous wood were observed on pine woody debris. • Generalist species and hyphomycetous fungi were more tolerant of bird impact. • A shift in fungal assemblages was recorded three years after the start of bird impact.