Soil fungi have pivotal ecological roles as decomposers, pathogens and symbionts. Alterations to their diversity arising from climate change could have substantial effects on ecosystems, particularly those undergoing rapid warming that contain few species. Here, we report a study using pyrosequencing to assess fungal diversity in 29 soils sampled from a 1,650 km climatic gradient through the maritime Antarctic, the most rapidly warming region in the Southern Hemisphere.