Forestry is known to have clear negative effects on the diversity of fungal species, especially on those that are producing large, long living fruitbodies. However, the effect of forestry has not been comprehensively studied among different fungal groups and host tree species in boreal forests. Also most often a study plot based approach has been utilized in which the substrate quality is always very different between the managed and unmanaged forests. In the present study, we studied the effect of forestry on fungal assemblages inhabiting large logs of similar quality among the different management classes. We included all non-lichenized fungal species producing sexual fruitbodies on 42 decaying logs of Betula spp., Picea abies, Pinus sylvestris, and Populus tremulae in 6 mature and 6 natural forests, totaling 192 logs. The detected fungi were split into groups based on the morphology of their fruitbodies, namely agarics, discomycetes, pileates, pyrenomycetes, ramarioids, resupinates, stromatic pyrenomycetes, and tremelloids. We analyzed the effect of management and characteristics of the study logs to the total fungal species richness at site and log level. The effect was also tested separately for the different fruitbody groups and host tree species. We also analyzed how the above variables and their different combinations correlate with the composition of the fungal assemblages. We found 666 fungal taxa, out of which 546 occurred in the natural, and 486 in the mature sites. The average species richness of the total species data differed significantly at site and log level, natural forests having more species than mature forests but especially at the log level the effect was very weak. At site level the difference was mostly due to the discomycete group on Pinus, whereas at the log level due to the pileate group on Picea. For the majority of the groups we did not detect a significant effect of any of the variables. The composition of the total species assemblage was mostly explained by the tree species, bark cover and decay stage of the log. The most important variable or their combination explaining the composition varied depending on the fruitbody group and host tree species. To conclude, our study demonstrates the importance of considering different fungal groups and host tree species simultaneously in applied surveys. Different drivers for the observed trends can be revealed when comparing site and log level results. And finally, when the quality of the substrate is similar between the mature and natural forests the effect of forest management is still visible but the effect is very weak.