In order to establish a system for marker assisted selection (MAS) to develop new rice cultivars with good eating quality, we conducted QTL analyses for physicochemical properties of rice by using a recombinant inbred (RI) population consisting of 92 lines derived from a cross between closely related japonica cultivars, Moritawase (a cutivar with low eating quality) and Koshihikari (a cultivar with good eating quality). We developed a linkage map with 119 simple sequence repeat (SSR) markers. Physicochemical properties of rice were evaluated two years by measuring protein content, amylose content and textural characteristics. QTL analysis for protein content revealed three QTLs on chromosome 2, 6 and 9. Four QTLs for amylose content were detected on chromosome 3, 7, 9 and 12. One QTL for texture characteristics were identified on chromosome 3. The DNA markers linked to these QTLs will be used for the MAS for good eating quality.