In this study, differential expression of heat-stable proteins in eighty-five cultivated rice (Oryza sativa L.) was analyzed by using SDS-PAGE and western blotting, to explore the feasibility of using specific proteins to identify Indica-Japonica rice. The results showed that the heat-stable proteins expressed differentially between Indica and Japonica rice, especially in the molecular weight of about 42 kD ~ 47 kD range. Among them, 45.2 kD band (Band I) and 46.5 kD band (Band II) were marker bands for typical Japonica rice. Both bands matched to Os03g0168100 in NCBI protein databank, 42.0 kD band (Band Ⅲ, matched to OsI_10172) was marker band for typical Indica rice. Eighty-five Indica and Japonica rice varieties were identified based on the expression pattern of these three bands, and then compare the results with Cheng’s index. The concordances were 80.0% and 86.4% in typical Indica rice and Japonica rice, respectively. Therefore, the method of hest-stable protein marker bands can be used for identifying typical Indica rice and Japonica rice.