Investigating Saharan soil microbiomes via microbial community inventorying is crucial to our general understanding of the phylogenetic diversity of root-associated microbial communities and assemblages. This paper investigates the qualitative distribution of root-associated microorganisms of two date palm cultivars, one of which is resistant (Takerbucht) and the other susceptible (Aghamu) to Fusarium oxysporum f. sp. albedinis (F.o.a.) infection. Species richness comprised 314 bacterial strains belonging to four distinct taxonomical groups (Bacillus, Burkholderiales, Pseudomonas, and Coryneforms). Overall, 55, 141 and 118 isolates affiliated to 10, 12 and 13 different species were identified in control, young and old date palm rhizospheres, respectively. To better visualise the patterns of microbiome association, we combined a principal component method with a hierarchical-partitional clustering analysis, which allowed and facilitated interpretation of root assemblages by clustering comparable items together. In vitro antifungal activity showed that the isolates that had a strong antagonistic effect were the ones that predominated in the endorhizosphere of the Takerbucht cultivar. These bacteria were almost exclusively members of the genus Bacillus, especially B. subtilis, exhibiting notable antifungal activity against Fusarium oxysporum f. sp. albedinis in arid environments.