The abundant genetic diversity provides a broad genetic basis for soybean breeding. Based on 35 pairs of SSR markers, the genetic diversity of 60 soybeans being resistant to Phytophthora Root Rot in Northeast China was analyzed. A total of 189 alleles were detected, with an average of 5.4 alleles per locus. The polymorphism information content index (PIC) was variable from 0.1550 to 0.8195 with an average of 0.6636. The genetic similarity coefficient varies from 0.31 to 0.74. The fingerprint map in each of resistant varieties was constructed using 5 pairs of highly polymorphic SSR primers. Using NTSYS2.10 clustering analysis based on genetic distance, sixty resistant genotypes were divided into 7 groups, of which 78.33% of resistant varieties (lines) had a similarity coefficient between 0.45 and 0.74. That indicated a relatively narrow genetic difference among these resistance-conferring genotypes. The results of cluster analysis and population genetic structure analysis partially overlap, suggesting the existence of multiple penetration and communication events between resistant materials in different regions.