This study examined whether mutualism with different genotypes of nitrogen-fixing symbionts affected relative plant fitness in a natural environment. Amphicarpaea bracteata (Leguminosae) plants from eight populations were paired and transplanted into 86 small plots at a field site. Each 16 cm diameter plot contained three plants from each of two populations, and was inoculated with an isolate of Bradyrhizobium from the native site of one of the two host populations (chosen at random). The total seed biomass produced by plants from each host population within a plot was used as a measure of lifetime reproductive success. For three out of the four sets of paired competitors, there was a highly significant increase in relative fitness when plants grew in the presence of a Bradyrhizobium isolate from their native population. On average, substituting a native for a non-native bacterial genotype caused a 39% increase in seed biomass per plant (range among eight populations, -13% to +182%). These results indicate that differential compatibility of host and symbiont genotypes can be a significant factor controlling the fitness of competing plants in nature.