Seeds of 15 diverse rice accessions, representing aus, indica, temperate japonica and tropical japonica subpopulations, were produced under temperate climate conditions in Korea and used for vitamin E analysis and seed storage experiments at 45°C and 10.9% seed moisture content. High γ-tocotrienol was significantly positively correlated with seed longevity. In addition, a high β-tocopherol proportion relative to δ-tocopherol was significantly negatively correlated with seed longevity. Using high-density single-nucleotide polymorphism marker data, DNA haplotype analysis showed clear allelic variations in the region of two S-adenosylmethionine synthetase genes: LOC_Os04g42095 and LOC_Os11g15410, which regulate the conversion of δ-tocopherol into β-tocopherol. Four indica accessions with rare and subpopulation-specific alleles showed a 2.3-fold lower β-/δ-tocopherol ratio compared with accessions from other subpopulations.