Arbuscular mycorrhizae, ubiquitous mutualistic symbioses between plant roots and fungi in the order Glomales, are believed to be important controllers of plant responses to global change, in particular to elevated atmospheric CO2. In order to test if any effects on the symbiosis can persist after long-term treatment, we examined root colonization by arbuscular mycorrhizal (AM) and other fungi of several plant species from two grassland communities after continuous exposure to elevated atmospheric CO2 for six growing seasons in the field. For plant species from both a sandstone and a serpentine annual grassland there was evidence for changes in fungal root colonization, with changes occurring as a function of giant host species. We documented decreases in percentage nonmycorrhizal fungal root colonization in elevated CO2 for several plant species. Total AM root colonization (%) only increased significantly for one out of the five plant species in each grassland. However, when dividing AM fungal hyphae into two groups of hyphae (fine endophyte and coarse endophyte), we could document significant responses of AM fungi that were hidden when only total percentage colonization was measured. We also documented changes in elevated CO2 in the percentage of root colonized by both AM hyphal types simultaneously. Our results demonstrate that changes in fungal root colonization can occur after long-term CO2 enrichment, and that the level of resolution of the study of AM fungal responses may have to be increased to uncover significant changes to the CO2 treatment. This study is also one of the first to document compositional changes in the AM fungi colonizing roots of plants grown in elevated CO2. Although it is difficult to relate the structural data directly to functional changes, possible implications of the observed changes for plant communities are discussed.