Atmospheric CO2 and O-3 concentrations are increasing due to human activity and both trace gases have the potential to alter C cycling in forest ecosystems. Because soil microorganisms depend on plant litter as a source of energy for metabolism, changes in the amount or the biochemistry of plant litter produced under elevated CO2 and O-3 could alter microbial community function and composition. Previously, we have observed that elevated CO2 increased the microbial metabolism of cellulose and chitin, whereas elevated O-3 dampened this response. We hypothesized that this change in metabolism under CO2 and O-3 enrichment would be accompanied by a concomitant change in fungal community composition. We tested our hypothesis at the free-air CO2 and O-3 enrichment (FACE) experiment at Rhinelander, Wisconsin, in which Populus tremuloides, Betula papyrifera, and Acer saccharum were grown under factorial CO2 and O-3 treatments. We employed extracellular enzyme analysis to assay microbial metabolism, phospholipid fatty acid (PLFA) analysis to determine changes in microbial community composition, and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) to analyze the fungal community composition. The activities of 1,4-beta-glucosidase (+37%) and 1,4,-beta-N-acetylglucosaminidase (+84%) were significantly increased under elevated CO2, whereas 1,4-beta-glucosidase activity (-25%) was significantly suppressed by elevated O-3. There was no significant main effect of elevated CO2 or O-3 on fungal relative abundance, as measured by PLFA. We identified 39 fungal taxonomic units from soil using DGGE, and found that O-3 enrichment significantly altered fungal community composition. We conclude that fungal metabolism is altered under elevated CO2 and O-3, and that there was a concomitant change in fungal community composition under elevated O-3. Thus, changes in plant inputs to soil under elevated CO2 and O-3 can propagate through the microbial food web to alter the cycling of C in soil.