Soils suppressive to soil-borne diseases are defined by a low disease incidence in spite of the presence of a virulent pathogen and a susceptible plant. In many cases, the inhibition of the disease development relies on the activity of the resident soil microbiome. To identify taxonomic microbial indicators linked to the suppressiveness phenotype of soils, culture independent-based methods have been employed to analyse and compare microbial dynamics in two different soils suppressive to either Rhizoctonia solani damping-off disease of sugar beet or Fusarium wilt disease on flax. Fungal and bacterial taxonomic biodiversity were estimated from ITS and 16S genes by amplicon pyrosequencing. To that end, metagenomic DNA was extracted from the rhizosphere of plants grown in soils with different level of suppressiveness. We obtained 218650 reads in total (125602 for fungi and 93048 for bacteria). At this moment, the analyses of fungal communities are in progress. 114641 reads was kept after filtering by bioinformatic pipeline, distributed into 2303 clusters and 3379 singletons. Although, the bioinformatic and statistical analysis are not finished yet, we have already noticed a difference in the taxonomic diversity composition between suppressive and conducive soils which could explain the suppressive/conducive character of given soil. The next step is to achieve the bacterial communities in Fusarium wilt suppressive/conducive soils and to assess the microbial diversity of other soil-borne diseases suppressive soils. Once the analyses of sequencing data are finished and the taxonomic assignments done, the comparison of microbial diversity of all studied soils will be performed in order to find out the similarities or/and differences in these soils which will provide the suppressiveness indicators