Climate warming is leading to shrub expansion in Arctic tundra. Shrubs form ectomycorrhizal (ECM) associations with soil fungi that are central to ecosystem carbon balance as determinants of plant community structure and as decomposers of soil organic matter. To assess potential climate change impacts on ECM communities, we analysed fungal internal transcribed spacer sequences from ECM root tips of the dominant tundra shrub Betula nana growing in treatments plots that had received long-term warming by greenhouses and/or fertilization as part of the Arctic Long-Term Ecological Research experiment at Toolik Lake Alaska, USA. We demonstrate opposing effects of long-term warming and fertilization treatments on ECM fungal diversity; with warming increasing and fertilization reducing the diversity of ECM communities. We show that warming leads to a significant increase in high biomass fungi with proteolytic capacity, especially Cortinarius spp., and a reduction of fungi with high affinities for labile N, especially Russula spp. In contrast, fertilization treatments led to relatively small changes in the composition of the ECM community, but increased the abundance of saprotrophs. Our data suggest that warming profoundly alters nutrient cycling in tundra, and may facilitate the expansion of B. nana through the formation of mycorrhizal networks of larger size.