Soybean is an important oil- and protein-rich crop worldwide. It is vital to identify soybean genotypes that show tolerance at initial crop growth stages (germination to fourth tri-foliate leaf stage) that coincide with a heavy monsoon. A set of 964 diverse soybean accessions was evaluated for pregermination anaerobic stress (pGAS) tolerance for different durations (3, 5, 7 and 9 days) under the paper towel method in artificial conditions. After nine days of submergence, the EC accessions exhibited significantly higher percent germination (11%), followed by IC germplasm (8.11%), breeding lines (2.40%) and the commercial varieties (2.12%). Ninety-seven genotypes showing phenotypic variation during the initial screening were further evaluated for waterlogging tolerance in perforated cups, and germination percentage was recorded after nine days of stress treatment. Forty-five of these 97 genotypes surviving waterlogging tolerance were shortlisted to evaluate their performance under two field screening conditions in two locations. The accessions EC471972, EC471920 and EC472119 were identified as tolerant to eight days of waterlogging in the seed germination stage after four levels of screening. These selected accessions can be used as sources of pregermination anaerobic stress tolerance in breeding programs.