Peas (Pisum sativum L.) are exposed to waterlogging at germination when grown as relay in rice-based cropping. Ninety-one germplasm accessions were evaluated in relay (sown in waterlogged soil), and subsequently 10 diverse genotypes compared under relay and sole cropping (conventional tillage sowing) over two seasons in Bangladesh. Contrasting genotypes, BM-3, NL-2 and Kaspa, were further evaluated in three waterlogging treatments (drained control, 4 and 8 days waterlogging) in the glasshouse. Conspicuous variation in waterlogging tolerance at germination was observed in the field and confirmed under controlled conditions. In relay sowing in 2011, emergence of a few genotypes was affected by waterlogging. In 2012, emergence in relay was severely affected (12 plants/m2) compared to sole sowing (37 plants/m2). Among genotypes BM-3 had 6 plants/m2 emerge, which all subsequently died, in contrast to NL-2 in which emergence was 13 plants/m2 with all plants surviving. In the glasshouse, there was 14% emergence in BM-3, 40% in NL-2 and 55% in Kaspa after 8 days of waterlogging. Such marked differences in waterlogging tolerance at germination in the model pea are the first reported and illustrate prospects for selection to improve adaptation to relay sowing in South Asia.