Ecologists studying plant and animals have long recognized that the modifications of diversity across a landscape are central for understanding the environmental factors driving the magnitude and the variability of community assembly. Despite the statement that this conceptual vision is also relevant for microorganisms, since it can offer valuable insights into the relative influence of dispersal limitations, environmental heterogeneity, and environmental and evolutionary changes in shaping the structure of ecological communities, studies integrating wide spatial scale have been poorly investigated and the environmental filters structuring microbial biodiversity remain largely unknown. In this context, we have investigated the characterisation of indigenous microbial communities from soils sampled on a broad scale. This characterisation relied on analyses of density, diversity and genetic structure of microbial communities by using molecular tools directly on DNA extracted from the soil library of RMQS ("Rseau de Mesures de la Qualit des Sols" = French soil quality monitoring network) which cross-rules all the French territory with about 2,200 soils sampled. Geo-positioning, physico-chemical characteristics, climatic factors, floristic composition and land use of these soils were also recorded. The geostatistical interpolation of soil microbial density and diversity revealed a heterogeneous distribution of microbial communities on a wide extent which is spatially structured in bio geographical patterns. Microbial density and diversity seems to be more influenced by local filters such as soil properties and land use but is relatively independent of global filters such as climatic factors or the presence of natural barriers. Our study confirms that the biogeography of microorganisms differs fundamentally from the biogeography of "macro-organisms" and that soil management can have significant large-scale effects.