Elevated atmospheric CO2 generally increases plant productivity and subsequently increases the availability of cellulose in soil to microbial decomposers. As key cellulose degraders, soil fungi are likely to be one of the most impacted and responsive microbial groups to elevated atmospheric CO2. To investigate the impacts of ecosystem type and elevated atmospheric CO2 on cellulolytic fungal communities, we sequenced 10 677 cbhI gene fragments encoding the catalytic subunit of cellobiohydrolase I, across five distinct terrestrial ecosystem experiments after a decade of exposure to elevated CO2. The cbhI composition of each ecosystem was distinct, as supported by weighted Unifrac analyses (all P-values; < 0.001), with few operational taxonomic units (OTUs) being shared across ecosystems. Using a 114-member cbhI sequence database compiled from known fungi, less than 1% of the environmental sequences could be classified at the family level indicating that cellulolytic fungi in situ are likely dominated by novel fungi or known fungi that are not yet recognized as cellulose degraders. Shifts in fungal cbhI composition and richness that were correlated with elevated CO2 exposure varied across the ecosystems. In aspen plantation and desert creosote bush soils, cbhI gene richness was significantly higher after exposure to elevated CO2 (550 µmol mol−1) than under ambient CO2 (360 µmol mol−1 CO2). In contrast, while the richness was not altered, the relative abundance of dominant OTUs in desert soil crusts was significantly shifted. This suggests that responses are complex, vary across different ecosystems and, in at least one case, are OTU-specific. Collectively, our results document the complexity of cellulolytic fungal communities in multiple terrestrial ecosystems and the variability of their responses to long-term exposure to elevated atmospheric CO2.