Brazil is the largest producer and consumer of common bean worldwide, and the crop can benefit from its symbiosis with a variety of rhizobia by means of biological nitrogen fixation in root nodules. In this study, the role of Mesoamerican and Andean genotypes of common bean in trapping rhizobia directly from a Brazilian oxisol in the field or in pots in greenhouse conditions with unaltered or diluted soil solutions was investigated. Genetic diversity was evaluated by the profiles of BOX-PCR obtained, and by estimates of Shannon and Abundance-based Coverage Estimator (ACE) indices. Rhizobia trapped by Mesomaerican genotypes had greater diversity, reinforcing the hypothesis of an important and long-time contribution of this genetic center to the establishment of common bean in Brazil. Greater diversity was also seen in rhizobia trapped straight from the soil than from plants inoculated with diluted soil solutions, emphasizing a highly diverse and competitive rhizobial indigenous population. Studies on genetic diversity of common bean rhizobia are important not only for helping to understand the evolution of the legume-rhizobia symbiosis, but also to devise strategies to increase the contribution of the biological nitrogen-fixation process.