We evaluated whether geographic distance and soil characteristics influence genetic structure of nitrogen-fixing bacterial symbionts associated with the host plant Chamaecrista fasciculata (Partridge Pea). We tested phylogeographic clustering and associations between genetic distance, geographic distance, and soil variables using sequences of 2 bacterial genes and soil chemistry across 23 sites in Mississippi. We identified rhizobia isolated from Partridge Pea as Bradyrhizobium. We detected significant genetic structure at a regional level, and determined that rhizobia within each region were more phylogenetically related than expected. Significant correlation between genetic distance and distances based on soil chemistry suggests environmental influences on rhizobia diversity. High levels of diversity among rhizobia over small spatial scales suggest that symbionts respond to local factors. Understanding geographic diversity in natural assemblages of rhizobia aids in predicting how hosts and symbionts respond to environmental perturbations.