The temporal and spatial snow cover dynamics is the primary factor controlling the plant communities' composition and biogeochemical cycles in arctic and alpine tundra. However, the relationships between the distribution of snow and the diversity of soil microbial communities remain largely unexplored. Over a period of 2 years, we monitored soil microbial communities at three sites, including contiguous alpine meadows of late and early snowmelt locations (LSM and ESM, respectively). Bacterial and fungal communities were characterized by using molecular fingerprinting and cloning/sequencing of microbial ribosomal DNA extracted from the soil. Herein, we show that the spatial and temporal distribution of snow strongly correlates with microbial community composition. High seasonal contrast in ESM is associated with marked seasonal shifts for bacterial communities; whereas less contrasted seasons because of long-lasting snowpack in LSM is associated with increased fungal diversity. Finally, our results indicate that, similar to plant communities, microbial communities exhibit important shifts in composition at two extremes of the snow cover gradient. However, winter conditions lead to the convergence of microbial communities independently of snow cover presence. This study provides new insights into the distribution of microbial communities in alpine tundra in relation to snow cover dynamics, and may be helpful in predicting the future of microbial communities and biogeochemical cycles in arctic and alpine tundra in the context of a warmer climate.