Abstract：The composition and structure of rice grain starch are two major factors which influence the grain quality. In this study, we used 17 molecular markers based on sequence diversities between two rice subspecies, indica and japonica, to investigate the genotypes of 67 japonica cultivars. The results showed: all 67 japonica varieties carried the japonica allele Wxj. , and among 16 locus of amylopectin synethesis-related genes（ASRG）,13 locus had introgression of indica while the other 3 locus, GBSSⅡ, SSⅡ-2 and SSⅣ-1 , had no recombination. the frequency of indica allele introgression was from 1.9% to 46.27%, and SSⅠgene had the highest introgression frequency. Stepwise regression analysis demonstrated that 7 genes had effects on the 10 physico-chemical properties, including amylose content(AC), gel consistency(GC), starch RVA characteristics(RVA).And Isa gene had effects on peak viscosity( PKV), break down value(BDV), consistency value(CSV), setback value(SBV) and peak time(PeT)，while the other 6 genes only had obvious genetic effects on 1-4 characteristics. The results indicated that the functional differentiation had been occured on the ASRG locus. These results provided useful information for rice quality improvement.