Understanding plant-microbial interactions is essential in the process of revegetating marginal lands. The structures of the rhizospheric bacterial and fungal communities of 14 woody families growing in three contaminated environments (Pb, Cd, Zn, Mn, Fe, S) were characterized using high throughput sequencing. In this study, local plant varieties were chosen for their growth and adaptation. Among the 38 tree species, three were planted on all the three studied soils that differ in composition and structure, namely Carrières-sous-Poissy, Leforest and Thann, and their microbial communities were compared. The rhizospheric bacterial communities for a given site showed no significant difference between the various woody species, but differed greatly between sites. The Proteobacteria phylum was dominant with more than 25% of the relative abundance overall, followed by the Actinobacteria, Bacteroïdetes, Gemmatimonadetes. In contrast to the bacteria, fungal communities exhibited contrasting patterns between the sites and the tree species. The Betulaceae, Salicaceae and Fagaceae families gathered a great proportion of Basidiomycota, especially ectomycorrhiza, and the lowest diversity and richness. The other tree families (e.g. Platanaceae, Juglandaceae, Ulmaceae), as well as the unplanted soil, have more abundant Ascomycota and Mucoromycota communities. This study has also emphasis that trees select different bacterial and fungal communities depending on the site they were planted. The woody trees are thus able to select their microbial communities depending the environmental parameters. These results highlighted that the woody species have selected their fungal communities. These findings may have important implications for the successfully revegetation of marginal lands using microbial-based approaches