The objective of the study is to dissect genetic basis and identify QTL related to Anaerobic germination related traits in rice, and to detect the elite rice lines carrying favorable alleles, therefore providing excellent germplasm for molecular marker-assisted (MAS）breeding. The seeds of 318 rice lines were germinated for measuring coleoptile length under normal and anaerobic conditions. QTL associated with anaerobic germination (AG）tolerance was determined by GWAS and candidate genes were analyzed. The broad variation of AG tolerance was observed among rice accessions ranged from -0.923 to 3.069, with an average of -0.238, a median of -0.342. A total of 27 QTL revealed by 83 SNPs were detected associating with AG tolerance. The QTL locus qAG4-2 was selected for analyzed and 20 candidate genes in the target interval were annotated. Among them, three genes were detected with elevated transcripts induced by anaerobic stress. The excellent germplasm resources and the QTL loci associating with anaerobic germination were valuable in rice breeding.