To determine the genetic diversity characteristics small seed soybean varieties（lines） in Northeast China,21 pairs of SSR primers were used to analyze the genetic diversity of 44 small seed soybean varieties（lines） which were collected from different regions in Northeast China. The results showed that a total of 115 alleles were detected from 44 small seed soybean varieties（lines） in Northeast China and 3～11 alleles were detected at different SSR locus with an average of 5.5 alleles per SSR locus. The PIC ranged from 0.309 1 to 0.815 7 with an average of 0.629 7.Six pairs of highly polymorphic SSR primers were used to construct the fingerprints of 44 small seed soybean varieties（lines）, which could discriminate these 44 small seed soybeans efficiently. Pair-wise genetic similarity coefficients of 44 small seed soybean varieties（lines） ranged from 0.25 to 0.95. The cluster analysis showed that 44 small seed soybean varieties（lines） could be divided into five major groups, reflecting a certain genetic exchange between small seed soybean varieties（lines） from different regions.