Rice is the most important staple food crop of almost half of the world`s population. In rice, seed longevity is major factor for production and storage potential of seeds. But it is faced with grain degradation and loss of seed viability. Lipoxygenases(LOX) are a family of enzymes related to the seed longevity. LOX activity in rice grain is present in a bran-milling fraction. It is also observed that rice embryos contains three isozymes activites, Lox1, Lox2 and Lox3. Among those, the Lox3 isozyme is known as the major component in the embryonic tissue. In this study, genetic structure variability of three seed longevity related genes, Lox1, Lox2 and Lox3 were examined by using whole-genome resequencing data of 137 accessions of rice core set. The new SNPs and InDels in the exon regions identified through haplotyping analysis would be useful to develop new varieties with improved storage ability of rice in the future molecular breeding.