The diversity of a collection of 21 bradyrhizobial isolates from Lima bean (Phaseolus lunatus L.) was assayed by molecular methods. Moderately high to high genetic diversity was revealed by multilocus enzyme electrophoresis (MLEE) analysis of seven enzyme loci and genomic fingerprints with ERIC and BOX primers. Two groups with differences in growth rate were found among the isolates and their differentiation as two divergent bradyrhizobial lineages was supported by PCR-RFLP of the rpoB gene and sequence analysis of the 16S rDNA and dnaK genes. Isolates with slow growth (SG) were identified as Bradyrhizobium yuanmingense, while extra-slow growing isolates (ESG) constitute a new lineage different from all described Bradyrhizobium species. Three distinct symbiotic genotypes were detected among Lima bean bradyrhizobia by PCR-RFLP and sequence analysis of the nifH and nodB genes. One genotype was found in the ESG lineage and two in B. yuanmingense. Another symbiotic genotype was detected in B. yuamingense isolated from Lespedeza plants. The identified bradyrhizobial lineages constitute sympatric species effectively nodulating Lima bean on the coast of Peru.