Biofumigation was applied before the culture of carrots for two years on an experimental plot. Assessment of soil suppressiveness to Rhizoctonia solani damping-off showed that biofumigation increases the level of soil suppressiveness in comparison to the untreated control. Microbial analyses were performed on soil samples collected from each plot to compare both the density and the structure of the microbial communities. The fungal population density was higher in the biofumigated plot; moreover one fungal genus, Aspergillus, was dominant. Cloning and sequencing of the ITS region of the dominant Aspergillus colonies enabled us to identify the strains as A. fumigatus with 97 to 100 % of similarity. Terminal restriction fragment length polymorphism (T-RFLP) analysis applied to total DNA extracted from soil revealed a significant difference in the structure of the fungal communities between the biofumigated plot and the control. This difference was based on the presence of a few discriminating terminal restriction fragments (TRF). T-RFLP analyses applied to isolates of A. fumigatus enabled us to determine the TRF of this species, which fits perfectly with one of those revealed by T-RFLP analysis from soil DNA. Using both traditional microbiological techniques (soil plate dilution) and molecular tools enabled us to detect and identify one fungal population which is a marker of the biofumigation. Whether A. fumigatus is just a marker of biofumigation or is involved in the mechanisms controlling soil suppressiveness has still to be investigated.