Abstract: Using 39 Minghui derived lines from indica-japonica cross and 17 indica and japonica parents as materials,the heterotic grouping and the genetic diversity analysis were researched.The result of the cluster analysis with SSR molecular markers was similar to it of the cluster analysis with phenotype on accurately clustering dominant groups.However,the cluster analysis with phenotypic traits did not accurately indicate the relationship between tested materials but SSR markers did it at the molecular level.It suggests that the cluster analysis of SSR molecular markers could be applied to unknown materials in relationship for the heterotic grouping.SSR markers of 221 primer pairs were used to analyze genetic diversity of tested materials.The results showed that,the maximum values of Nei gene diversity index,Shannon diversity index and polymorphism information content(PIC) were all higher in the strains of indica-japonica cross than in parental values.The maximum value of Nei gene diversity index,Shannon diversity index,polymorphism information content(PIC) were 0.819,1.856,0.796 for the strains of indica-japonica cross,respectively,and 0.796,1.677,0.766 for their parents′respectively.It indicated that,by genetic selection,the allelic variation was more abundant in the strains of indica-japonica cross than in the parental.