We previously reported that extra-slow-growing Bradyrhizobium japonicum isolates obtained from three field sites in Japan, designated as HRS (highly reiterated sequence-possessing) strains, have high copy numbers of the insertion sequences RSalpha and RSbeta. When strain collections in the USA, Japan, Korea, Thailand and China were examined by Southern hybridization using RSalpha, RSbeta and IS1631 as probes, HRS strains were found in the Japanese, Chinese, and American collections, but not in the Korean and Thai ones. Copy number analyses of RSalpha and RSbeta, calibrated with the copy number of rrs (16S rRNA gene), indicated that the HRS stains can be divided into two major groups. Group A is comprised of members with a high copy number of RSalpha (mean+/-S.D., 139+/-27), a low number of RSbeta (mean+/-S.D., 30+/-13) sequences, and extremely slow growth rates (mean doubling time+/-S.D., 27+/-9 h). In contrast, group B is comprised of strains with a high copy number of RSbeta (mean+/-S.D., 93+/-6) and a lower number of RSalpha. These groupings of HRS strains were well correlated with phylogenetic clusters based on rrs, gyrB and serogroups (110/122 and 123/135). Growth rate of B. japonicum strains was also correlated exclusively with RSalpha copy number. The ecological, evolutionary and biotechnological implications of the findings are discussed.