One hundred and fifteen varieties (including cultivars and lines) with different ecotypes in japonica rice (Oryza sativa L.) were analyzed for endosperm storage proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to estimate their genetic diversity for the purpose of genetic improving and variety identification. Nineteen types of profile were identified according to 1) presence/absence of 65 kDa bands, 2) staining intensity of 70, 60, 57, 37-39, 22-23, 13 and 10 kDa bands, 3) migration velocity of 35 kDa (α-4) and 4) band number at 57 kDa location. An unweighted-pair group average method with arithmetic mean (UPGMA) dendrogram based on the cluster analysis of genetic similarity of the protein bands showed a small genetic variation among the tested materials, with the similarity coefficients varying between 0.75 and 1.00. Three distinct groups were identified from the cluster analysis of the rice varieties studied at the similarity coefficient level of 0.894. The first group included eight varieties with high amylose content, the second group contained fifteen varieties with high protein content, and the third group had the remaining ninety-two varieties, which accounted for 80% of the total materials. Clear relationship between ecotypes distinguished by maturity and groups revealed by cluster analysis was not found in this study. Only the group of high amylose linked with medium-maturity medium japonica ecotype. The bands of 70 kDa and 65 kDa can be used as protein markers to identify F1 seed purity of japonica hybrid rice Liuyanyou 422. One hundred and fifteen varieties (including cultivars and lines) with different ecotypes in japonica rice (Oryza sativa L.) were analyzed for endosperm storage proteins by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) to estimate their genetic diversity for the purpose of genetic improvement and variety identification. Nineteen types of profiles were identified according to 1) presence / absence of 65 kDa bands, 2) staining intensity of 70, 60, 57, 37-39, 22-23, 13 and 10 kDa bands, 3 ) un unweighted-pair group average method with arithmetic mean (UPGMA) dendrogram based on the cluster analysis of genetic similarity of the protein bands showed a small genetic variation among the tested materials, with the similarity coefficients varying between 0.75 and 1.00. Three distinct groups were identified from the cluster analysis of the rice varieties studied at the similarity coefficient level of 0.89 4. The first group included eight varieties with high amylose content, the second group contained fifteen varieties with high protein content, and the third group had the remaining ninety-two varieties, which accounted for 80% of the total materials. Clear relationship between ecotypes distinguished by maturity and groups revealed by cluster analysis not not found in this study. Only the group of high amylose linked with medium-maturity medium japonica ecotype. The bands of 70 kDa and 65 kDa can be used as protein markers to identify F1 seed purity of japonica hybrid rice Liuyanyou 422.