QTL mapping of germinability under submergence condition and pyramided effect analysis of stable sites were carried out， thus laying a foundation for fine mapping of QTL for germinability under submergence condition and marker-assisted breeding. Using an F_2：3 population with 144 individuals derived from a cross between WR-4 （a weedy rice with strong germinability under submergence condition） and Guangbaixiangzhan （a susceptible indica variety， GBXZ）， a high density genetic map containing 825 bin markers was produced based on 1K mGPS SNP chip. Ten QTL conferring tolerance to hypoxia were identified by complete interval mapping （ICIM）. These QTL were found on chromosomes 3， 4， 7， 8， 9， and 10， with LOD values ranging from 3.6 to 21.3， explaining phenotypic variation of 3.0%-21.1%. Two major QTL （qGS4-1 and qGS7-1） with high LOD value and high phenotypic variance were repeatedly detected， and both loci could be the candidate for future gene cloning studies. According to the genotyping of bin markers in each QTL interval， different progenies were classified into WR type and GBXZ type. By further data processing and analysis of QTL stacking， it was found that individuals with more pyramided synergistic alleles showed longer coleoptile under submergence condition. Thus， these lines hosting multiple synergistic alleles might provide innovative resources for breeding rice cultivars with high germinability under submergence condition.