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The acreage of submerged direct-sown cultivation of Oryza sativa is gradually increasing in China because of the constantly decreasing number of laborers in rural areas. Identifying favorable alleles for seedling anoxic tolerance (SAT) is necessary for improving cultivars suitable for submerged direct-sown rice cultivation. In this study, we used two populations to detect quantitative trait loci (QTLs) for SAT. In the natural population consisting of 542 accessions, seven simple sequence repeat marker loci associated with SAT were detected in both 2016 and 2017, with 22 favorable alleles. RM5340 on chromosome 2 and RM6811 on chromosome 6 were newly identified. Allele RM6811-160 bp had the largest phenotypic effect (1.09 cm/cm). Seventy-one accessions carried this allele. In the backcross inbred line population (115 lines) derived from Wuyunjing 7 hao/Ludao//Wuyunjing 7 hao, 8 QTLs for SAT were detected, with the phenotypic variance explained (PVE) ranging from 2.51 to 12.11%. The qCELpc2, qCELpc3, qCELpc5 and qCELpc11 loci were newly detected. The favorable alleles of loci qCELpc3, qCELpc5 and qCELpc11 were from Ludao. The locus qCELpc11 had the largest PVE of 10.39%, with a substitutive effect of 0.82 cm averaged over 2 years. By sequencing the gene locus OsBIERF, which was within a 15.50–16.08 Mb chromosome region harboring SAT-associated RM3600 on chromosome 9 and was detected in both populations, a single nucleotide polymorphism locus at the first exon was found between Wuyunjing 7 hao (T) and Ludao (C). The favorable alleles detected in this study could be used to improve SAT of rice cultivars. [ABSTRACT FROM AUTHOR]