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The fundamental understanding of diversity, composition and functions of biological communities and their ecological drivers has long been recognized as essential for the study of climate change and its implications for ecosystems. Despite significant advances on our understanding of the dynamics of animal and plant communities and how they respond to environmental variability, little is still known about belowground dynamics, particularly those involving ectomycorrhizal (EM) fungi that play pivotal roles in soil nutrient cycling and plant nutrition. This mutualistic symbiosis is the dominant plant-fungus association in alpine ecosystems, which are among the most threatened by experiencing rapid change as a consequence of climatic shifts and human-related activities. Therefore, to better understand the resilience of these ecosystems to climate variability, it is of paramount importance to study the EM fungal communities that help sustain these habitats. In this thesis I aim to generate baseline diversity data and investigate the biotic and abiotic drivers of alpine EM fungal communities across the European Alps. To do this I assessed the EM fungal communities in the soil and roots of i) 47 populations of Dryas octopetala, Bistorta vivipara and Salix herbacea across altitudinal and environmental gradients in 5 countries of the Alps and ii) from 87 willows across a hybrid zone between Salix purpurea and Salix helvetica in the Rhône glacier valley. The results reveal that alpine and sub-alpine habitats harbour a high diversity of EM fungi mostly dominated by lineages with non- or inconspicuous reproductive structures such as Tomentella-Thelephora, Sebacina and Cenococcum. Moreover, alpine EM fungal communities are mostly generalists and functionally redundant, influenced by fine-scale habitat changes in edaphic properties, like soil pH and total nitrogen, rather than elevation or biotic variables such as host phylogeny (at family or genus level). This thesis provides important contributions to our understanding of the diversity and ecology of belowground alpine EM fungal communities in the European Alps and how they may respond to future environmental change. It is expected that the outcomes of this study aid the development of management and mitigation plans to tackle the decline of unique alpine habitats in the face of a changing climate.