Amylose in rice is controlled by granule-bound starch synthase, a protein encoded by the Waxy (Wx) gene. This study was conducted to identify the polymorphisms in the partial Waxy gene for two BC2F7 and nine BC4F3, breeding lines and their parents, Oryza sativa cv. MR219 and O. rufipogon, and also the association between the polymorphism of the partial Waxy gene and the amylose content. Sequences of all 13 breeding lines showed that the microsatellite (CT)17 located 55bp upstream of the 5’-leader intron splice site and had G at the first nucleotide of the splice donor site of intron 1 of the Wx gene. The amylase content analysis revealed that all the samples with similar (CT)17 were in the intermediate category (20–25%), except for one BC2F7 line (19%). The genotype determined using the microsatelites and SNP markers supports the intermediate category of the amylase content values.