The cell densities and the genetic structure of bacterial pools present in the various microenvironments of a silt loam soil has been investigated. The microenvironments were isolated first using a procedure of soil washes (Ranjard et al., 1997) which separated bacteria located outside and at the surface of aggregates (outer part) from those located inside aggregates (inner part). A non-destructuring physical fractionation (Kabir et al., 1994) was then applied to the inner part in order to separate bacteria located inside aggregates of different size, stability, physical and chemical characteristics. Bacterial densities measured by direct counts and viable heterotrophic cell enumerations permitted to show the heterogeneous quantitative distribution of bacterial cells with a higher abundance in the inner part compared to the outer part and a higher abundance in the microaggregate fractions and the dispersible clay fraction of the inner part than in other size-fractions. The rRNA intergenic spacer analysis (RISA) was used to study the genetic structure of the bacterial pools. Distinct fingerprints and consequently different genetic structures were obtained between the unfractionated soil and the microenvironments and also between the various microenvironments. Cluster and multivariate analyses showed the close relationships between the two macroaggregate fractions, between the two microaggregate fractions and between the outer part and the dispersible clay fraction. These analyses also highlighted the influence of clay and organic matter content on the genetic structure relatedness.