Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused byXanthomonas oryzaepv.oryzae(Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperateJaponicaaccessions inoculated with two ChineseXoostrains (KS6-6 and GV) and one PhilippineXoostrain (PXO99A). Based on the 55K SNPs Array dataset of the 359Japonicaaccessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. SixRgenes were localized in theqBBV-11.1,qBBV-11.2, andqBBV-11.3loci on chromosome 11 in thisJaponicacollection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably,LOC_Os11g47290inqBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype ofLOC_Os11g47290exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.