Soil houses a huge biodiversity involved in ecological services through microbial community assembly. However, processes driving soil microbial community assembly are still scarcely understood, particularly the relative importance of environmental heterogeneity regarding to dispersal limitations. This can be achieved through studying the determinism of taxa-area relationship (TAR, how community composition change with geographic distance), a fundamental relationship in ecology. Here, a biogeographical approach was applied on a wide scale to evaluate TAR for soil bacterial and fungal communities and to partition their spatial variations into environmental heterogeneity effects and dispersal limitations effects. Four contrasted regions, extracted from the French soil quality monitoring network, were considered: Brittany, Burgundy, Landes and South-East. The genetic structure of indigenous bacterial and fungal communities was determined by molecular fingerprinting and their TARs were evaluated. Significant TARs were observed in Brittany and South-East for both bacteria and fungi, and only for bacteria in Burgundy. The turnover rates of bacterial and fungal communities were in the same order of magnitude between regions and microbial groups despite different environmental patterns among regions. Distance-based canonical redundancy analysis was used to confront genetic data to soil physico-chemical characteristics, climatic conditions, land use and site location (a descriptor for dispersal limitations). Spatial variations of soil bacterial and fungal communities’ assembly were mainly explained by environmental heterogeneity (15% to 36% of variance). Dispersal limitations explained smaller but significant amounts of variance in only two regions (ca. 3%). Among environmental factors, pH ranked first but their hierarchy changed with region and organism type.