Proteomic analyses of soybean seedlings responding to flooding were conducted to identify proteins involved in such response. Soybean was germinated for 48 h and then subjected to flooding stress for 6-48 h. Proteomic analysis of hypocotyl and root was used in a time-dependent manner, and altered proteins were identified using soybean protein data file constructed for this research. Under flooding stress, 35 proteins were up-regulated, whereas 16 proteins were down-regulated at a 24-h time point. Changes in energy generation was recognized because several glycolytic enzymes were up-regulated. General stress response was also shown to occur as various reactive oxygen species scavengers were up-regulated. Other identified proteins with diverse functional categories suggest that flooding stress includes not only hypoxic stress, but also other stresses such as weak light, disease, and water stresses. In addition, proteins with unknown functions were shown to be positioned as hubs which activate other proteins in system response networks by protein-protein interaction analysis, suggesting that this type of interaction analysis is useful for screening of important factors in plant response to environmental stresses.