The long-term effects of rising atmospheric carbon dioxide (CO2) and tropospheric O3 concentrations on fungal communities in soil are not well understood. Here, we examine fungal community composition and the activities of cellobiohydrolase and N-acetylglucosaminidase (NAG) after 10 years of exposure to 1.5 times ambient levels of CO2 and O3 in aspen and aspen–birch forest ecosystems, and compare these results to earlier studies in the same long-term experiment. The forest floor community was dominated by saprotrophic fungi, and differed slightly between plant community types, as did NAG activity. Elevated CO2 and O3 had small but significant effects on the distribution of fungal genotypes in this horizon, and elevated CO2 also lead to an increase in the proportion of Sistotrema spp. within the community. Yet, although cellobiohydrolase activity was lower in the forest floor under elevated O3, it was not affected by elevated CO2. NAG was also unaffected. The soil community was dominated by ectomycorrhizal species. Both CO2 and O3 had a minor effect on the distribution of genotypes; however, phylogenetic analysis indicated that under elevated O3Cortinarius and Inocybe spp. increased in abundance and Laccaria and Tomentella spp. declined. Although cellobiohydrolase activity in soil was unaffected by either CO2 or O3, NAG was higher (∼29%) under CO2 in aspen–birch, but lower (∼18%) under aspen. Time series analysis indicated that CO2 increased cellulolytic enzyme activity during the first 5 years of the experiment, but that the magnitude of this effect diminished over time. NAG activity also showed strong early stimulation by elevated CO2, but after 10 years this effect is no longer evident. Elevated O3 appears to have variable stimulatory and repressive effects depending on the soil horizon and time point examined.