Abstract: Soil and soybean cultivar are the main factors that influence genetic diversity of rhizobia. In this study, we isolated a total of 149 fast-growing and 49 slow-growing nodule bacteria strains from four soybean cultivars grown in soils with two different crop rotations by plant trapping method. We used amplified 16S rDNA restriction analysis (ARDRA), restriction fragment length polymorphism (RFLP) analysis of 16S-23S intergenic spacer (IGS) gene and nod C gene to investigate the effects of crop rotation and soybean cultivar on genomic diversity of rhizobia. ARDRA showed two rDNA types. Type Ⅰ covered all fast-growing strains belonged to Sinorhizobium, while type Ⅱ contained all slow-growing strains belonged to Bradyrhizobium. Three patterns constituted IGS-RFLP-IGS pattern Ⅰ identical to B. liaoningense of slow-growing strains, IGS pattern Ⅱ and IGS pattern Ⅲ similar to two reference strains of S. fredii of fast-growing strains. Based on the results for 16S-23S IGS ARDRA and RFLP, slow-growing strains were identified as B. liaoningense and fast-growing strains identified as S. fredii. Percent average of S. fredii in soils with winter wheat as fore-rotating crop (95.18%) was much higher than that in soils with maize as fore-rotating crop (53.78%), and this varied in relation to different soybean cultivars. In both soil types, 'Jidou 12' showed the highest affinity for S. fredii. Correlation analysis between IGS genotypes of 198 strains and host soybean cultivars showed that 'Wuxing 1' cultivar was most correlated to IGS type Ⅰ (Bradyrhizobium), 'Williams' and 'Jidou 17' cultivars most correlated to IGS type Ⅱ (Sinorhizobium) and 'Jidou 12' cultivar most correlated to IGS type Ⅲ (Sinorhizobium). Results for C-RFLP node showed that crop rotation and soybean cultivar did not affect the nodulation genotype of strains. The results from this study revealed some interactions among rhizobia, crop rotation and soybean cultivar. The effect of crop rotation on rhizobium species was greater than that of soybean cultivar. Soybean cultivar showed some selectivity for rhizobium genotype.