Random amplified polymorphic DNA (RAPD) assay was used to distinguish strains of Sclerotinia sclerotiorum with different characteristics and its related species S.trifoliorum strain Ywd-A, S. minor strain 3-4-1 and unknown species strain Let-19. The results showed that 8 out of 40 primers (10-mer) could stably amplify the genomic DNA from the tested strains.Analyses of amplified polymorphic DNA fragments showed that similarity coefficients between the tested strains of S.sclerotiorum were 0.5052-0.7931,whereas those between 7 strains of S. sclerotiorum and 3 strains representing other two species of Sclerotinia and Let-19 were 0.1942-0.3853.In UPGMA phenogram, Let-19 is located between S.trifoliorum strain Ywd-A and S.minor strain 3-4-1 with regards to phylogenetic relationships with strains of S.sclerotiorum. Seven strains of S.sclerotiorum were classified into three groups, but the classifi-cation was not related to their biological characteristics. It is concluded from this research that RAPD assay can be used to evaluate genetic diversity of S. sclerotiorum and to disclose phylogenetic relationship in Sclerotinia species.