In boreal forests, the level of naturalness and the stage of succession explain most of the variation in forest structure within a particular forest type. Thus, these two factors should also have a major effect on species assemblages in forests, at least on species groups associated with wood. The present study is the first attempt to analyze empirically the simultaneous effects of forest succession and naturalness on wood-inhabiting fungi, a taxonomic group of special ecological importance. The study area was situated in eastern Finland, middle boreal zone. A total of 41 study plots were established in Pinus sylvestris forests representing three levels of forest naturalness: natural, seminatural and intensively managed forests. Five stages of succession were distinguished according to the age of the dominating tree layer (<10, 40, 70, 110, and >150 yr old), except in managed forests where only four stages were available. A total of 5328 records of 195 species of fungi were made. The first, open stage of succession was clearly the most species-rich period of succession in all levels of forest naturalness. In natural and seminatural forests, the first stage of succession was also very distinctive in its fungal composition, and thus of special value in protecting biodiversity in boreal forests. In the succession following the first stage, the level of naturalness had more effect on assemblages of fungi than did the stage of succession. Intensive forest management affects threatened species particularly. In conclusion, natural young stages of succession should also be included in the network of boreal forest reserves.