Fungi of woody debris are a diverse and functionally important component of forest ecosystems, but are potentially threatened by forest management activities. We used fruiting body and molecular sampling of the nrLSU gene to compare the composition and richness of fungal communities between 2 decay classes of conifer logs (classes 1 and 4) and among boreal mixedwood sites from 3 management histories (mechanized clearcutting, horse-based clearcutting, and unlogged). In 5 sites per management type, 5 logs per decay class were sampled for fruiting bodies. Wood samples for DNA extraction were collected from the logs at 3 mechanized logged and 3 unlogged forest sites. Fruiting body surveys yielded 116 species; 34 from decay class 1 logs, 65 from decay class 4 logs, and 17 from both. Molecular sampling, based on selection of 20 clones per log, yielded 304 operational taxonomic units (OTUs); 97 from decay class 1 logs, 184 from decay class 4 logs, and 23 from both. Community composition differed strongly between the 2 decay classes both for the fruiting body and OTU samples, with more species being recovered from decay class 4 than decay class 1 logs. Community composition also significantly varied according to log diameter and volume for fruiting bodies. The number of fruiting bodies on decay class1 logs was significantly greater in unlogged than logged sites and also was positively correlated with site-level volume of recently-decayed conifer woody debris. Dacrymyces chrysospermus and Fomitopsis rosea were significantly more frequently encountered in unlogged than logged stands. Despite relatively large volumes of woody debris in the logged stands that we sampled, we obtained evidence that logging in these forests resulted some 30–60 years later in a reduction in the amount and diameter of early-decay coniferous downed wood, with reductions in fungal fruiting body diversity as a result.