In order to study genetic structure of strains of Rhizobium leguminosarum bv. trifolii recovered from some species of clover in soils of different parts of Iran, soil samples were collected from various geographical regions of the country, including Lorestan, Isfahan, Khorasan, Hamedan, Kermanshah, Kordestan and West Azerbaijan. Clover species including Bersim clover, Persian clover and Red clover were grown in these soils. Following nodulating soil Rhizobia on the host roots, bacteria were isolated from nodules and a bacterial collection containing 420 isolates was provided. Strains of R . leguminosarum bv. trifolii were characterized using BOX-PCR fingerprinting method. At first, the isolates from each 21 soil-species treatments were compared. Second step of comparison was performed among selected isolates of the first step in each soil sample and final step of caparison was done between isolates from different soil samples. The number and frequency of isolates was determined using strain richness and strain dominance indices. Natans soil-Persian clover treatment with strain richness of 0.62 showed the most diversity among all the investigated treatments. Kermanshah soil sample with SR of 0.33 and Lorestan soil sample with the SR of 0.12 were the most and the least diverse soil samples respectively. The values of strain richness for the clover species were estimated 0.3 for Red clover, 0.28 for Persian clover and 0.23 for Bersim clover. From 152 isolates that were investigated in this study, 23 strain types relating to three clover species recognized, which strain number 9 with SR of 0.16 was the most dominant strain of all. Profile generated by BOX-PCR was used to estimate genetic similarity of the strains, using Jacard similarity coefficient, and a cluster was constructed according to UPGMA method at NTSYS.2.0 software. Comparison of similarity coefficients and relating dendrogram did not reflect any special relation between strain of rhizobia strain, clover species and soil sample. In order to investigate phylogenetic relationships, strains were characterized by RFLP of recA gene. Results indicated that all the isolates belong to the same specie. Also the strains were subjected to melanin production and salt resistant tests, which the results of the two were negative. A primer mocDEF/ mocDER was employed in order to detection of rhizopine activity in the R. leguminosearum bv. trifolii strains recovered from Iranian clovers. None of the isolates investigated.