To test whether Rhizobium loti are coadapted to nodulate local plant genotypes, we competed R. loti strains in a common environment with clonally propagated Lotus corniculatus. Both the plants and bacterial strains were originally collected from natural populations in three localities and the R. loti strains used were distinguishable by enzyme electrophoretic markers and differed in geographical origin relative to host plant origin. The proportions of nodules occupied by symbiont strains varied widely and depended on both host plant and symbiont genotype. Nonrandom nodulation patterns resulted primarily from preferential nodulation of host genotypes by the symbiont strain that had been associated with the host in the natural environment. Symbionts nodulating their original hosts were preferentially found in nodules on adventitious tap roots as opposed to the younger, lateral roots (for one host-symbiont pair) or in large nodules, independent of location on the root system (for a second host-symbiont pair). The proportion of nodules occupied by a symbiont on novel host genotypes varied, ranging from nearly random expectation to a significant reduction in the proportion of nodules occupied. The analysis of the bacteria recovered from 994 nodules by multilocus enzyme electrophoresis revealed that 952 (95.8%) nodules were occupied by one of the four inoculant strains and 11 (1.1%) were co-occupied by two inoculant strains. A total of 31 (3.1%) nodules were occupied by strains that did not match the electrophoretic profiles of the original inoculant strains. Based on the comparison of multilocus profiles for 23 enzyme loci, we concluded that these bacteria were foreign strains and not recombinants of the original inoculant strains. Our findings indicate a strong host genotype by strain interaction underlying the outcome of rhizobial competition for nodulation sites and suggest there are distinct mechanisms leading to differential recognition of compatible host and symbiont genotypes.