Soil fungal communities are likely to be central in mediating microbial feedbacks to climate change through their effects on soil carbon (C) storage, nutrient cycling, and plant health. Plants often produce increased fine root biomass in response to elevated atmospheric carbon dioxide (CO2), but the responses of soil microbial communities are variable and uncertain, particularly in terms of species diversity. In this study, we describe the responses of the soil fungal community to free air CO2 enrichment (FACE) in a semiarid chaparral shrubland in Southern California (dominated by Adenomstoma fasciculatum) using large subunit rRNA gene sequencing. Community composition varied greatly over the landscape and responses to FACE were subtle, involving a few specific groups. Increased frequency of Sordariomycetes and Leotiomycetes, the latter including the Helotiales, a group that includes many dark septate endophytes known to associate positively with roots, was observed in the FACE plots. Fungal diversity, both in terms of richness and evenness, increased consistently in the FACE treatment, and was relatively high compared to other studies that used similar methods. Increases in diversity were observed across multiple phylogenetic levels, from genus to class, and were distributed broadly across fungal lineages. Diversity was also higher in samples collected close to (5 cm) plants compared to samples in canopy gaps (30 cm away from plants). Fungal biomass correlated well with soil organic matter (SOM) content, but patterns of diversity were correlated with fine root production rather than SOM. We conclude that the fungal community in this ecosystem is tightly linked to plant fine root production, and that future changes in the fungal community in response to elevated CO2 and other climatic changes will be primarily driven by changes in plant belowground allocation. Potential feedbacks mediated by soil fungi, such as soil C sequestration, nutrient cycling, and pathogenesis, are discussed.