One hundred and four isolates of BRADYRHIZOBIUM JAPONICUM were isolated from nodules of two different trap plants, Viz. Soya bean cultivars, Maple Glen and Orford which were inoculated with two different soil samples (Ottawa and St-Hugus soils). All isolates were clustered based on PCR/RFLP of 16S-23S rRNA genes. RFLP analysis was performed to characterize all the isolates using six different endonuclease enzymes. The data was analyzed by using Jamp software. Using dendrogram data, all the isolates were grouped into six different clusters. There were four and five clusters of BRADYRHIZOBIUM JAPONICUM in Ottawa and St-Hugus soils, respectively. Three clusters were common between two cultivars of Soya bean when inoculated with Ottawa soil and four common clusters were recognized when trap plants inoculated with St-Hugus soil. In Ottawa soil, cluster I was not detected by Orford cultivar, likewise in St-Hugus soil, cluster VI was not detected by Maple Glen cultivar of Soya bean. Isolates of cluster III were dominantly trapped when Maple Glen and Orford cultivars inoculated with Ottawa soil but isolates from clusters I, IV and III were trapped when they were inoculated with St-Hugus soil. Since different cultivars trapped different isolate types it can be concluded that for population studies of rhizobial bacteria different trap plants can provide a better composition of native population of bacteria.