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Peanut (Arachis hypogaea L.) is a legume crop native from South America and grown worldwide. This is well adapted to the unfavorable edaphoclimatic conditions found in Brazilian Semi-Arid region, where is cultivated mainly by smallholders. The selection of new rhizobial isolates is important to increase the rates of biological nitrogen fixation and yield. Furthermore, the diversity evaluation of new bacterial isolates may help us to understand the ecology of these groups in regions where little information are available. In this context, this study aimed to evaluate the phylogenetic relationships of peanut bradyrhizobia from Brazilian Semi-Arid soils by analysis of 16S rRNA, recA, nodC and nifD gene sequences, as well as their symbiotic performance. A trap-host experiment was performed using two soil samples from the municipality of Barbalha, Ceara, Brazil, taken under peanut cropping and one soil sample from the municipality of Juazeiro, Bahia, Brazil, covered by the native Arachis triseminata. Seeds of peanut cv. BR1 were sown and the plants were grown until 52 days after emergence. The nodules were inoculated in YMA medium for isolation of slow-growing bacteria. The Box-PCR fingerprinting and the 16S rRNA gene sequences was evaluated for all bacteria and recA, nodC and nifD were sequenced for the six selected isolates. Selected bacteria were evaluated according to their symbiotic characteristics in a greenhouse experiment. Ten slow-growing isolates were obtained and classified within the genus Bradyrhizobium, by the 16S rRNA sequence analysis and showed divergent Box-PCR profiles. All bacteria were clustered within the B. japonicum clade. The bacteria from Juazeiro were closely related to B. yuanmingense, and those from Barbalha showed similarity to B. yuanmingense, B. kavangense and B. guangxiense. The sequences of recA showed partial congruence to the 16S rRNA gene analysis but the phylogeny trees based on the symbiotic genes were not related, indicating horizontal gene transfer. All bacteria were able to efficiently nodulate the peanut and the isolate ESA 83, pointed out regarding the nitrogen fixation ability and were selected for further analysis in non-sterile soils and field conditions.