The physicochemical properties of starch, such as apparent amylose content, gelatinization temperature, and pasting viscosities, determine the eating, cooking, and processing qualities of various products of rice. A recombinant inbred line (RIL) population derived from the reciprocal cross of Lemont (a premium high-quality tropical japonica rice) and Jiayu 293 (a high-yield but low-quality indica rice) was used to test the association of microsatellite markers of starch-synthesizing genes with starch quality parameters. The results confirmed the association of Wx and starch synthase I (SSI) alleles with various starch properties measured in rice flour. However, the starch properties were not associated with the starch branching enzyme 1 (SBE 1) gene alleles.