Soybean [Glycine max. (L.) Merr] is one of the most important legumes in the world. However, soybean varieties are sensitive to flooding stress and their seed yields are substantially reduced in response to the flooding stress. 192 soybean germplasm collection was screened to identify flooding tolerant germplasm at an early vegetative growth stage (V1). Soybean plants at V1 stage were waterlogged for 4 to 10 days. To evaluate flooding tolerance, survival rate were investigated as a time dependent manner. Jangbaegkong, Danbaegkong, Sowonkong, Socheong2 and Suwon269 showed flooding tolerance, while Shillog, T201, T181, NTS1116 and HP-963 showed flooding sensitivity. We also investigated effects of flooding stress on soybean morphology. The adventitious root development was greatly increased in flooding tolerant plants compared to it in flooding sensitive plants. In addition, root length and root number were analyzed. The significant reduction of root length and root number was observed in flooding sensitive plants. Thus, these results indicate that the morphological changes in roots are important for acclimation to flooding stress. Taken together, the relationship between the morphological changes in the roots and flooding tolerance may be useful in selecting a flooding tolerant soybean germplasm.