MostOryza sativacultivars die within a week of complete submergence-a major constraint to rice production in south and southeast Asia that causes annual losses of over US$1 billion and affects disproportionately the poorest farmers in the world1,2. A few cultivars, such as theO. sativassp.indicacultivar FR13A, are highly tolerant and survive up to two weeks of complete submergence owing to a major quantitative trait locus designatedSubmergence 1(Sub1) near the centromere of chromosome 9 (refs3-6). Here we describe the identification of a cluster of three genes at theSub1locus, encoding putative ethylene response factors. Two of these genes,Sub1BandSub1C,are invariably present in theSub1region of all rice accessions analysed. In contrast, the presence ofSub1Ais variable. A survey identified two alleles within thoseindicavarieties that possess this gene: a tolerance-specific allele namedSub1A-1and an intolerance-specific allele namedSub1A-2.Over-expression ofSub1A-1in a submergence-intolerantO. sativassp.japonicaconferred enhanced tolerance to the plants, downregulation ofSub1Cand upregulation ofAlcohol dehydrogenase 1(Adh1), indicating thatSub1A-1is a primary determinant of submergence tolerance. The FR13ASub1locus was introgressed into a widely grown Asian rice cultivar using marker-assisted selection. The new variety maintains the high yield and other agronomic properties of the recurrent parent and is tolerant to submergence. Cultivation of this variety is expected to provide protection against damaging floods and increase crop security for farmers.