Submergence is becoming a major problem in decreasing rice production. This study conducted a QTL analysis for submergence tolerance on germination stage using 165 recombinant inbred lines (RILs) derived from crosses between ‘Milyang 23’ and ‘Tong 88-7’. An integrated genetic linkage map consisting of 1,313 SNPs was constructed, which covered a total length of 1,254.59 cM, with an average distance of 0.96 cM between adjacent markers. Four QTLs were detected on chromosomes 1, 3, 4, and 7. In qSUB1 and qSUB3, the allele of ‘Tong88-7’ improved survival rates, while in qSUB4 and qSUB7 the allele of ‘Milyang 23’ improved the same. Phenotypic variance explanations for qSUB1, qSUB3, qSUB4, and qSUB7 were 9.44%, 14.62%, 9.74%, and 7.09%, respectively. The average survival rate of the lines with all four QTLs was 93.33±6.67%.