Excess soil moisture induces hypoxia, causing waterlogging injury in soybeans [Glycine max (L.) Merr.]. Twelve Japanese soybean cultivars with varying hypoxia tolerance were used. Of these, 11 (all but Hayahikari) were evaluated for waterlogging tolerance using a scaled index with data from previous studies. To investigate hypoxic responses, cultivars were grown under hydroponic conditions for 2 wk a year for 2 yr, with aerobic or hypoxic oxygen concentrations artificially maintained in the rhizosphere. Hypoxic responses (measured as plant dry weight and root morphology) were assessed at the early vegetative stage. The effects of hypoxic treatment on root dry weight were significant, and the effect of year on soybean dry weight was not significant. The change in root dry weight, and particularly, in coarse root length, was significantly correlated with waterlogging tolerance index at the 0.001 probability level. This study showed that root responses to rhizosphere hypoxia might reflect waterlogging tolerance in soybeans.