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Bakanae disease is caused by several species of Fusarium and imposes serious limitations on rice production worldwide. The incidence of this disease is increasing in the top rice-growing countries. Thus, higher resistance to this disease may be a cost-saving solution preferable to the application of fungicides. Here, we developed 168 near-isogenic rice lines (NILs, BC6F4) to locate a QTL for resistance against bakanae disease. The lines were derived from a cross between Shingwang, a highly resistant variety (indica), and Ilpum, a highly susceptible variety (japonica). The 24 markers representing the Shingwang allele in a bakanae disease-resistant NIL, YR24982-9-1 (parental line of the BC6F4 NILs), were located on chromosome 1, 2, 7, 8, 10, 11, and 12. Single marker analysis using an SSR marker, RM9, showed that a major QTL is located on chromosome 1. The QTL explained 65 % of the total phenotype variation in BC6F4 NILs. The major QTL that designated qBK1 was mapped in 520 kb region between RM8144 and RM 11295. The identification of qBK1 and the closely linked SSR marker, RM9, could be useful for improving rice bakanae disease resistance in marker-assisted breeding.