The nodulation tendency of indigenous soybean bradyrhizobia on Rj-genotype soybean cultivars was investigated using approximately 260 bradyrhizobia isolated from an Andosol with 13 soybean cultivars of five Rj-genotypes (non-Rj, Rj2Rj3, Rj3, Rj4 and Rj2Rj3Rj4). A dendrogram was constructed based on restriction fragment length polymorphism analysis of the polymerase chain reaction products (PCR-RFLP) of the 16S–23S rDNA internal transcribed spacer (ITS) region. Bradyrhizobium USDA strains were used as a reference. The dendrogram indicated nine clusters based on similarities among the reference strains. The ratio of beta diversity to gamma diversity (H′β/H′γ), which represents differences in the bradyrhizobial communities by pair-wise comparison between each cultivar, was obtained from Shannon–Wiener diversity indices. The results showed that bradyrhizobial communities among the same Rj-genotype cultivars were similar to each other, whereas bradyrhizobial communities between the Rj2-genotype and non-Rj, Rj3 or Rj4-genotype cultivars were significantly different. These results suggest that the Rj2-gene might not only affect the nodulation compatibility between Rj-genotype soybeans and bradyrhizobia, but also the nodulation tendency of the bradyrhizobia.