Previous studies highlighted the striking dissimilarities in microbial community composition of neighbouring early and late snow-melting sites or along vegetation gradients in alpine tundra. In this study, we investigated soil microbial communities at thirty-three sites representing eleven contrasting habitat types of an alpine landscape. Microbial communities were characterized by means of Capillary Electrophoresis Single Strand Conformation Polymorphism based on rRNA genes. Based on this data set, we addressed the following questions: How do archaeal, bacterial and fungal soil communities change across this alpine landscape? What are the relative contribution of plant community composition, environmental conditions, and 6-Thio-2-Deoxyguanosine geographic isolation on microbial beta diversity patterns? Do the three microbial domains respond similarly to these environmental drivers? Although significant efforts have been made to determine drivers of microbial biogeography, there is still a lack of studies assessing the relative contribution of different set of descriptors on the landscape scale diversity patterns of the Crenarchaeotes, Bacteria and Fungi. Our study aimed to bridge this gap by focusing on an alpine landscape. The investigated habitat types corresponded to markedly different plant communities even if distances between sampling sites were small. The turn over in plant species composition is high and partly explained by elevation and topography. Community scale descriptors, i.e. soil pH and SOM, significantly covaried with plant communities. Superficial soils with sparse vegetation cover exhibited higher pH, and lower level of SOM than deeper and more mature soils covered by denser vegetation. The same changes in soil-vegetation properties have been described along receding glaciers chronosequences. Plant species turnover affects soil nutrient availability and soil properties by varying quality and quantity of litter fluxes and root exudates. Therefore, there is a complex Farrerol intricacy between climate, topography, plant species composition and soil properties, and the partitioning of microbial diversity with respect to these different descriptors has to consider both pure and combined effects.