Overgrazing and climate change have resulted in the expansion of marginal lands and the deterioration of soil quality, leading to a decline and extinction of numerous Fabaceae species. In this context, particular attention was given to study the symbiotic interactions between native legumes and their associated microbiome, as a sustainable alternative for restoring vegetation cover and reestablishing soil fertility in vulnerable areas. The main objective of this study was to isolate and characterize the root nodules endophytes from 15 wild legumes, originating from diverse Tunisian climatic zones (humid, arid, and Saharan). The taxonomic diversity of the isolates was determined by means of morphological, genomic, and phylogenetic analyses based on molecular screening by BOX-PCR and sequencing of 16S rRNA and atpD genes. To further assess the symbiotic characteristics of certain isolates, we proceeded with the amplification of nodC and nodZ genes. In a collection of 210 strains, phylogenetic analysis revealed the presence of 46 rhizobial strains distributed among 6 genera, namely Rhizobium, Bradyrhizobium, Sinorhizobium, Mesorhizobium, Neorhizobium, and Agrobacterium. Our results showed the predominance of Sinorhizobium genus in arid and Saharian zones of southern Tunisia, represented by three different symbiovars: sv. meliloti, sv. Tunisiaense, and sv. Vachelliae. However, no nodC genes were detected in Bradyrhizobium, which was only present under humid climate suggesting the impact of environmental conditions on the diversity of the rhizomicrobiome and its symbiotic interaction with wild legumes. In addition, various non-rhizobial isolates were identified, including strains from α-, β-, and Gamma-proteobacteria, Firmicutes, and Actinobacteria. These strains were not only highly tolerant to different abiotic stresses, but also presented different plant growth promoting features (PGP), making them perfect candidates to boost the survival and productivity of food legumes in drylands.