Rice is the main food of the world. Due to the worldwide climate change, it has become an important topic for food security. Meanwhile, the molecular marker assisted selection applied in breeding program also becomes more and more popular. In this study, we used 7 molecular markers to genotypes of the 24 rice Taiwanese cultivars and the introgression lines carrying flooding-tolerance (Sub1 gene). The results demonstrated that only RM23887 displayed the polymorphisms between Taiwanese rice varieties and Sub1-introgression lines. Therefore, this marker can be used as a tool to distinguish with the genotypes of Taiwanese cultivars and their crossing progeny for improving the efficiency of breeding.