The distribution of the soil microbial diversity depends on a broad range of environmental filters nested in spatial scales from continent to millimeter. Although microbial biogeography studies have recently shown the influence of environmental factors (texture/pH/plant cover and land-use) on soil microbial abundance and diversity, little is still known about spatial heterogeneity at a micro-scale within soil. Our study aims at describing and understanding the distribution of abundance and diversity of soil microbial communities between different soil microenvironments. Four soils were selected on the basis of differences in physico-chemical properties and historical land-management practices. Soil microenvironments were obtained by applying a non-destructive soil fractionation procedure based on size separation of particles and water-stable aggregates (2000-250/250-63/63-20/20-2µm and <2µm classes). Total Soil and microenvironments physico-chemical characteristics were described (pH/C/N/texture). Microbial communities were described using: molecular microbial biomass (soil-DNA yield), bacterial and fungal density (real-time qPCR), genetic structure of bacterial and fungal communities (ARISA analysis) and, bacterial and fungal taxonomic inventory (pyrosequencing-based analysis of 16S & 18S rRNA gene regions). Our study allowed (i) the description of the spatial distribution of microbial communities at a microscale in different soil types and of the contribution of microenvironments’ diversity to the overall biodiversity of soil, (ii) to evaluate, for the first time, the taxa-area relationship for soil microorganisms at a microscale and, (iii) to rank the environmental filters structuring sub alpha-diversity of soil microbial communities in comparison with filters highlighted in biogeographical studies and therefore to answer the question “which filter for which scale”.