ABSTRACT.- Waterlogging is a critical abiotic stress increasing in importance due to more intense, erratic rainfall associated with climate change. Waterlogging leads to significant yield losses in sensitive crops, such as soybean (Glycine max [L.] Merr.). Identifying soybean genotypes and traits associated with better waterlogging tolerance is of high interest. We assessed the response of six soybean genotypes, selected from a field screening of over 190 genotypes, to 10 days of waterlogging at the R1 (onset of flowering) and R4 (grain filling) stages. We evaluated yield and its components, as well as shoot and root dry weights (DW) at the end of the waterlogging treatments and at maturity, along with morphological traits such as plant branch number, stem diameter and plant height. By integrating all these traits, a waterlogging tolerance index (WTI) was calculated for each genotype to rank their sensitivity. The WTI showed variations among genotypes from 0.61 to 0.77, indicating genotypic variation in response to waterlogging. Greater reductions in root DW compared to shoot DW were observed immediately after waterlogging. By maturity, shoot DW of waterlogged plants was more severely reduced than root DW in all genotypes. Despite similar DW losses at R1 and R4 at physiological maturity, seed number per plant and 100-seed weight responses differed between the treatments. Genotypes that performed well under control conditions suffered significant yield reductions of 70%-85% after waterlogging, mainly due to fewer fertile nodes and seeds per pod, with some also experiencing a notable decrease in 100-seed weight. In contrast, other genotypes had milder responses, with less severe reductions in seed and pod traits. Identifying breeding soybean genotypes tolerant to waterlogging during reproductive stages that maintain the number of fertile nodes and pods per node without changes in seeds per pod could significantly mitigate yield losses from waterlogging. © 2024 Wiley-VCH GmbH. Published by John Wiley & Sons Ltd.