The weakened seed germination ability under hypoxic conditions is the main limiting factor for direct seeding application， elucidating the genetic base of hypoxic germination tolerance is therefore essential for ensuring yield stability in direct-seeded rice systems. In this study， a mapping population was constructed using the cultivars Aigela and Xudao 10. Genotyping was performed using the rice 1K mGPS SNP chip， and a high-density genetic linkage map contains 595 Bin markers was developed. Through QTL mapping analysis， a total of nine QTLs for hypoxic germination tolerance， each explaining 4.61%-11.79% of the total phenotypic variation， were detected with LOD scores ranging from 2.57 to 5.49. Among these loci， five are previously reported loci related to hypoxic germination tolerance， and four loci were newly identified. By combining gene functional annotation， Arabidopsis homologous gene comparison， gene expression analysis， sequence comparison and qRT-PCR validation within the mapping interval of qHG6-2， a candidate gene （LOC_Os06g31280） related to hypoxic germination tolerance was identified which encodes a thionin protein， OsTHION1. Taken together， our findings provide a foundation for future cloning of hypoxic germination tolerance genes and dissecting their genetic regulatory mechanisms in rice.