This experiment was conducted to clarify the functions of supernodulating characters on seed yield determination through the comparison of agricultural traits of supernodulating soybean mutants, Kanto100, SS2-2, and their parent cultivars, Enrei and Shinpaldalkong2. The supernodulating soybean mutants Kanto100, SS2-2 were previously characterized by their superior capabilities of nitrogen (N) fixation and photosynthesis, and thereby it is expected to offer high yields. However, it is likely to be susceptible to waterlogging during the vegetative growth stage, which frequently occurs in major soybean producing areas. The presentstudy was intended to show the effects of waterlogging on nodulation, N fixation, photosynthesis and growth of Kanto100 and SS2-2.The supernodulating cultivar Kanto100 and its normally-nodulating parental cultivar Enrei, grown in pots,were subjected to waterlogging treatment that was imposed at the successive three vegetative growth stages for two years,2005 and 2006. The waterlogging treatment significantly reduced the number and weight of nodules of both cultivars, and the magnitude of the reduction was more pronounced in Kanto100 and SS2-2. The acetylene reduction activity (ARA) of nodules and apparent photosynthetic rate (AP) of leaves were generally depressed immediately after waterlogging treatment, but both functions exhibited remarkable recovery at the pod-filling stage irrespective of cultivar. No marked cultivar difference was found in the magnitudeof the reduction of ARA per plant and AP measured immediately after waterlogging and at the pod-filling stage irrespective of year, but growth impairment was more pronounced in Kanto100 and SS2-2 in one of the two years. These results indicate that Kanto100 and SS2-2 exhibits a marked decrease in dry matter production by waterlogging, but yield decrease is compensated to level similar to that of Enrei and Shinpaldalkong2 because of its enhanced nodule growth during the recovery stage. The supernodulating cultivar Kanto100 and SS2-2 is more susceptible to waterlogging under certain growing conditions than their normally-nodulating parent cultivar.