Rhizobia are one of the best-studied symbionts of leguminous plants, with high efficiency in biological nitrogen fixation and able to supply up to 90% of the plant nitrogen needs. Among legumes from tropical dry forests, Clitoria brachystegia Beth. (Fabaceae) is endemic to this ecosystem and its bacterial symbionts have never been reported. This study aimed to establish the diversity and nitrogen fixation potential of rhizobia isolated from C. brachystegia root nodules found in tropical dry forest remnants. The use of molecular techniques like BOX-PCR and 16S ribosomal gene sequencing, allowed the identification of 24 Rhizobium and 22 Bradyrhizobium strains which showed differential geographic distribution with most Rhizobium being recovered from Ecuador and all Bradyrhizobium from Peru. Diversity varied between sampling sites but no significant relationships were found with soil characteristics or climate conditions. Several Rhizobium and Bradyrhizobium strains showed good nitrogen fixation potential and thus may represent valuable resources in future conservation efforts of C. brachystegia, an endangered plant species.