QTL mapping of germinability under submergence condition and pyramided effect analysis of stable sites were carried out to lay 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 with 825 bin markers was constructed based on 1K mGPS SNP chip. As a result, ten QTL conferring tolerance to hypoxia were identified by complete interval mapping (ICIM), which were located 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%. Among them, two major QTL (qGS4-1 and qGS7-1) with high LOD value and high phenotypic variance, were repeatedly detected, and these two loci could be the candidate loci for subsequent gene function studies. According to the genotyping of bin markers, different progenies were divided into WR type and GBXZ type in each QTL interval. Further data processing and analysis were performed to analyze the pyramided effect of QTL. It was found that individuals with more pyramided synergistic alleles showed longer coleoptile under submergence condition. The identified lines with multiple synergistic alleles provide innovative resources for breeding rice cultivars with high germinability under submergence condition.