Bacterial strains isolated from root nodules on Acacia mangium at various locations in Indonesia were characterized by restriction fragment length polymorphism (RFLP) analysis of PCR-amplified 16S rDNA and by an intergenic repetitive extragenic palindromic (REP) sequence. The RFLP-16S rDNA analysis used four restriction endonucleases classified into seven Sau3AI, eight TaqI, nine HinfI, and nine MspI groups. Analysis of the amplified REP-PCR products showed intra-specific variations in the rhizobial genomic DNA. From the data obtained, 10 of the 15 strains isolated from A. mangium were classified as Bradyrhizobium. These isolates clustered with B. elkanii, and were predominant in the A. mangium nodulation systems. Partial 16S rDNA sequence analysis of some representative strains demonstrated that the RFLP clusters were stable and phylogenetically relevant.