Tongil (IR667-98-1-2) rice, developed in 1972, is a high-yielding rice variety derived from a three-way cross between indica and japonica. Tongil contributed to staple food self-sufficiency of Korea, an achievement that was termed the ‘Korean Green Revolution’. In this study, we analyzed the nucleotide-level genome structure of Tongil rice and compared it to those of the parental varieties. A total of 17.3 billion Illumina Hiseq reads, 47× genome coverage, were generated from Tongil rice. Three parental accessions, two indica and one japonica types, of Tongil rice were also sequenced for approximately 30x genome coverage. A total of 2,149,991 SNPs were detected between Tongil and Nipponbare; the average SNP frequency of Tongil was 5.77 per kb. Genome composition based on the SNP data by comparing with the three parental genome sequences on sliding window of Nipponbare genome sequence revealed that 91.8% of the Tongil genome originated from the indica parents and 7.9% from the japonica parent, different from the theoretical expectation in a three-way cross, i.e., 75% indica and 25% japonica parental origins on average. Copy number of SSR motifs, ORF gene distribution throughout the whole genome, gene ontology (GO) annotation, yield-related QTLs or gene locations, and polymorphic transposon insertions were also comparatively analyzed between Tongil and parents using sequence-based tools. The results indicated that each genetic factor was transferred from parents into Tongil in proportion to the whole-genome composition. The Tongil rice is the first successful superior cultivar derived from indica × japonica hybridization in Korea. Defining of genome structure demonstrates that the Tongil genome is composed mostly of the indica genome with a small proportion of japonica genome introgression. This work was supported by a grant from the Next-Generation BioGreen 21 Program (Plant Molecular Breeding Center No. PJ008125), Rural Development Administration, Republic of Korea.