Five species of Acacia (Acacia ehrenbergiana Hayne, A. nilotica (L.) Delile, A. seyal Delile, A. tortilis (Forssk.) Hayne and A. laeta Delile) indigenous to Tamanrasset (Algeria) were investigated for their nodulation status and nodular endophytic diversity. A. ehrenbergiana showed the highest nodulation ability across the different sites in this region, indicating the widespread occurrence of compatible rhizobia in the soils. Altogether 81 strains were purified. Among this endophytic strain collection, only four bacterial endophytes nodulated their respective host plants. On the basis of partial 16S rDNA sequencing, they were affiliated to Ensifer sp., Ensifer teranga, Mesorhizobium sp. and Rhizobium sp. Among the 79 non- symbiotic endophytes, 24 representative strains on the basis of PCR-RFLP profile obtained with MSPI enzyme digestion were characterized. They belonged to nine genera, namely: Paenibacillus, Ochrobactrum, Stenotrophomonas, Pseudomonas, Microbacterium, Rhizobium, Agrobacterium, Brevibacillus and Advenella. The isolated nodular endophytes in this study revealed a strong tolerance profile to salinity and high temperature. Principal component analysis confirmed that no correlation was found between bacterial tolerance to a maximum temperature of growth and soil depth of sampling. This tolerance profile was distributed over the three levels of soil depth sampling: 20, 40 and 60 cm. On the other hand, there was no relationship between in vitro tolerances of rhizobial strains to NaCl and high temperature and corresponding edaphoclimatic characteristics of the sampling sites. This study is a contribution to nodular bacterial diversity knowledge of desert African Acacia species growing in preserved ecosystems.