The rhizosphere microbiota emerges as a novel component that expands plant adaptation to its environment, and thus paves the way for future breeding approaches. Knowledge regarding the "functional core microbiota", which refers to the microbial taxa bearing essential functions for holobiont fitness, are required to move forward in this area. The aim of the present study was to compare the functional microbiota recruited by different plant genotypes in order to identify its core and variable components. Seven genotypes of Medicago truncatula (DZA315-16, DZA315-26, DZA045-6, F83005-5, SA028064, Jemalong A17 and J6), representatives of a core collection of 184 genotypes, were studied. Functional genes have been described using shotgun metagenomics followed by Prodigal. Core and variable functional microbiota have been identified based on shared genes and on genes explaining differences among the genotypes, respectively. Functional assignment has been obtained based on proteins annotation and Gene Onthology using BlastX and EggNOG. 76,264 genes were shared, whilst 3547 genes explained the differences between the three DZA genotypes and SA, 4662 among the three DZA and the F, A17, J6 genotypes, and 32 among SA and the three genotypes F, A17, J6. 60.5% of these genes have been assigned to biological processes, 22.6% to cellular components and 16.9% to molecular functions. Particularly, inorganic ion, amino-acid, and carbohydrate transport were the more represented in biological processes. This global analysis shows that different genotypes modulate rhizosphere microbial functional genes and provides new insights into the variable and core microbiota among different plant genotypes.