Resistant starch is beneficial for comsumer’s health. This research aimed to improve rice variety and develop molecular marker linked to resistant starch content in rice. The correlations between resistant starch content and molecular marker specific to SSIIIa, Waxy and SBEIIb gene which reported affecting on resistant starch content were tested in F2 population from two crossing, RD-Maejo 2 x RD 43 which are glutinous and non-glutinous rice respectively, and Pathum Thani 1 x Chao Lueang which are both non-glutinous rice. The results showed that the resistant starch content of 100 F2 samples from RD-Maejo 2 x RD 43 significantly correlated with marker specific to Waxy gene (r = 0.704, p < 0.000) and non-glutinous rice contained more resistant starch content than glutinous rice. Likewise, the resistant starch content of 92 F2 samples from Pathum Thani 1 x Chao Lueang significantly correlated with marker specific to Waxy gene (r = 0.682, p < 0.000). Rice with high amylose allele from Chao Lueang had more resistant starch content than rice with low amylose allele from Pathum Thani 1. The results indicated that the amylose content was positively related to the resistant starch content in rice. Molecular marker of Waxy gene linked to resistant starch content in rice and, therefore, it is suitable for selection of rice to increase resistant starch content. In addition, 100 seeds of BC1F1 were produced.