Pigeonpea is an important legume crop of the semi-arid tropics. In India, pigeonpea is mostly grown in areas prone to waterlogging, resulting in major production losses. It is imperative to identify genotypes that show tolerance at critical crop growth stages to prevent these losses. A selection of 272 diverse pigeonpea accessions was evaluated for seed submergence tolerance for different durations (0, 120, 144, 168 and 192 h) under in vitro conditions in the laboratory. All genotypes exhibited high (0·79–0·98) survival rates for up to 120 h of submergence. After 192 h of submergence, the hybrids as a group exhibited significantly higher survival rates (0·79) than the germplasm (0·71), elite breeding lines (0·68) and commercial varieties (0·58). Ninety-six genotypes representing the phenotypic variation observed during laboratory screening were further evaluated for waterlogging tolerance at the early seedling stage using pots, and survival rates were recorded for 8 days after completion of the stress treatment. Forty-nine of these 96 genotypes, representing the phenotypic variation for waterlogging tolerance, were chosen in order to evaluate their performance under natural field conditions. The following cultivated varieties and hybrids were identified as tolerant after three levels of testing (in vitro, in pots and in the field): ICPH 2431, ICPH 2740, ICPH 2671, ICPH 4187, MAL 9, LRG 30, Maruti, ICPL 20128, ICPL 332, ICPL 20237, ICPL 20238, Asha and MAL 15. These materials can be used as sources of waterlogging tolerance in breeding programmes.