We have determined that repetitive (repetitive extragenic palindromic [REP] and enterobacterial repetitive intergenic consensus [ERIC]) sequences used in conjunction with the polymerase chain reaction technique (REP and ERIC PCR) provide an effective means of differentiating between and classifying genetically related Bradyrhizobium japonicum serocluster 123 strains. Analysis of REP and ERIC PCR-generated dendrograms indicated that this technique can effectively differentiate between closely related strains which were indistinguishable by using other classification methods. To maximize the genomic differences detected by REP and ERIC PCR fingerprint patterns, the REP and the ERIC data sets were combined for statistical analyses. REP-plus-ERIC PCR fingerprints were also found to provide a method to differentiate between highly diverse strains of Bradyrhizobium spp., but they did not provide an effective means for classifying these strains because of the relatively low number of REP and ERIC consensus sequences found in some of the bradyrhizobia. Our results also suggest that there is a relationship between nodulation phenotypes and the distribution of REP and ERIC consensus sequences within the genomes of B. japonicum serogroup 123 and 127 strains. Results obtained by restriction fragment length polymorphism hybridization analyses were correlated with the phylogenetic classification of B. japonicum serocluster 123 strains obtained by using REP and ERIC PCR.