The genetic diversities of 25 soybean varieties were studied by ISSR markers, 9 polymorphic primers were selected from 28 ISSR primers, 65 bands were amplified with 9 primers, they contained 58 polymorphic bands and their polymorphism percentage was 89.23%; Shannon’s index evaluation indicted that average Shannon’s index was 0.4604 and the numbers of effective alleles were 1.5139; the genetic similarity coefficient among the 25 varieties ranged from 0.4462 to 0.8923, and the average GS was 0.6692; cluster analysis with UPGMA method showed that the cultivars tested in this study could be divided into five groups at the level GS 0.698.