Plants host in their rhizosphere a remarkable diversity of microorganisms that in return promote plant growth and health. Thus, the plant microbiota emerges as a novel component that expand the capacity of plants to adapt to the environment, and thus pave the way for future breeding approaches. It is widely known that different plant species harbor different microbiota, but very few studies showed an impact of the plant genotypes on the microbiota. These contrasting results may depend on the choice of the tested genotypes. We formulate the hypothesis that only those plant genotypes showing high genetic diversity and expressing different phenotypes harbor different rhizosphere microbiota and are able to modulate the microbial functioning. In this study, we aimed to assess a possible relation between the genetic/phenotypic diversity within Medicago truncatula and their associated microbiota. Seven M. truncatula genotypes were chosen on the basis of their geographical origin, genetic and phenotypic (notably their different nutritional strategies) diversity. Plant biomass and the carbon and nitrogen content in shoot and root were measured in order to describe their phenotypes. Microbial taxonomic diversity and functional genes were analysed through 16S rRNA amplicon and shotgun metagenomic, respectively. Results show that the seven plant genotypes clustered in three different phenotypes. The taxonomic diversity and functional genes of bacterial communities differed according to the plant cluster from which they are issued. These differences were explained by the following proteins: (i) Transposase from family Tn3 (bacterial plasmids remobilization), (ii) Membrane receptor TonB dependent (iron) and (iii) metallopeptidases from families TldD/PmbA and M14. Interestingly, TonB dependent transporter proteins seem to be involved in plant-microbe interactions (as this outer membrane protein binds and transports ferric chelates called siderophore, as well as various plant carbohydrates). These results support our initial hypothesis and show that contrasting genotypes modulate microbial gene abundance.