Abstract: The rhizobial DNA was extracted from the root nodules of soybean plants at a 6-year experiment site on black soil, and PCR-DGGE and clone sequencing were adopted to analyze the effects of different fertilization treatments on the diversity of soybean rhizobia. In the treatment no fertilization, the band number of nifH gene and the diversity indices were the highest, and there existed significant differences in the diversity indices among different treatments, with the order of no fertilization > high application rate of organic manure > low application rate of organic manure, 1/2 organic manure plus 1/2 chemical fertilizer > high application rate of chemical fertilizer > low application rate of chemical fertilizer. Cluster analysis demonstrated that the fingerprints in treatments of chemical fertilization only had a similarity of 66% with those in other treatments, suggesting that chemical fertilization could significantly alter the community structure of soybean rhizobia. The PCR-DGGE and clone sequencing showed that most of the rhizobia were belonged to Bradyrhizobium. The application of organic manure and chemical fertilizer, especially the latter, could decrease the diversity of soybean rhizobia.