Responses of the mycorrhizal fungal community in terrestrial ecosystems to global change factors are not well understood. However, virtually all land plants form symbiotic associations with mycorrhizal fungi, with approximately 20% of the plants' net primary production transported down to the fungal symbionts. In this study, we investigated how ericoid mycorrhiza (ErM), fine endophytes (FE) and dark septate endophytes (DSE) in roots responded to elevated atmospheric CO2 concentrations and warming in the dwarf shrub understory of a birch forest in the subarctic region of northern Sweden. To place the belowground results into an ecosystem context we also investigated how plant cover and nutrient concentrations in leaves responded to elevated atmospheric CO2 concentrations and warming. The ErM colonization in ericaceous dwarf shrubs increased under elevated atmospheric CO2 concentrations, but did not respond to warming following 6 years of treatment. This suggests that the higher ErM colonization under elevated CO2 might be due to increased transport of carbon belowground to acquire limiting resources such as N, which was diluted in leaves of ericaceous plants under enhanced CO2. The elevated CO2 did not affect total plant cover but the plant cover was increased under warming, which might be due to increased N availability in soil. FE colonization in grass roots decreased under enhanced CO2 and under warming, which might be due to increased root growth, to which the FE fungi could not keep up, resulting in proportionally lower colonization. However, no responses in aboveground cover of Deschampsia flexuosa were seen. DSE hyphal colonization in grass roots significantly increased under warmer conditions, but did not respond to elevated CO2. This complex set of responses by mycorrhizal and other root-associated fungi to global change factors of all the fungal types studied could have broad implications for plant community structure and biogeochemistry of subarctic ecosystems.