Geographic variation in the mutualism between the legume Amphicarpaea bracteata and its nitrogen-fixing root nodule bacteria (Bradyrhizobium sp.) was analyzed by sampling genotypes from II sites separated by distances ranging from 0.6 km to more than 1000 km. Cross inoculation experiments revealed that plants were genetically differentiated in traits determining compatibility with mutualist partners from different sites. Combinations of plant and bacterial genotypes native to the same local habitat yielded 26% higher plant growth relative to non-native combinations (range across 4 experiments; 9% to 48%). Among non-native symbioses, plant growth was unrelated to the geographic distance between sites of plant and bacterial origin. However, compatibility varied significantly with the genetic distance among host populations (inferred by multilocus enzyme electrophoresis): genetically similar plants from separate sites showed superior growth with each other's mutualist partners. Nevertheless, the tree structure of population genetic similarity was not congruent in plants versus bacteria. This implies that adaptive variation in symbiotic compatibility has evolved without strictly parallel divergence in the two species.