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Bakanae disease (BD), caused by the fungal pathogen <i>Fusarium fujikuroi</i>, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, &#8216;Samgwang&#8217; and &#8216;Junam&#8217;, respectively. Resequencing of &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, <i>qFfR9</i>, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24&#8722;7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the &#8216;Junam&#8217; and &#8216;Samgwang&#8217; genome sequence data, and are possibly candidate genes for <i>qFfR9</i>; therefore, <i>qFfR9</i> could be utilized as a valuable resource for breeding BD-resistant rice varieties.