This experiment was conducted to compare the tolerant responses between two soybean cultivars Sowonkong (tolerant) and Hannamkong (sensitive) when these were subjected to flooding stress. Plants were grown under photoperiod of natural light with day temperature of 30.6±5.3℃ and night temperature of 22.2±1.7℃. Flooding, filled with tap water to 1 cm above the level of the soil surface, was experimented for nine days when plants were at the vegetative (V4 to V5) and reproductive (R2; flowering) stage. The photosynthesis and transpiration of soybean with flooding declined progressively in comparison with the non-flooding at V4 to V5 and R2 stage. The Fv/Fm ratio and chlorophyll content also showed a constant decrease by the progressive flood stress. The photosynthesis, transpiration, Fv/Fm ratio and chlorophyll content were more affected by the flooding in Hannamkong than in Sowonkong. The NH_4 content increased up to five days after flooding but thereafter, rapidly decreased at both stages except for Sowonkong flooded at V4 to V5 stage. The NO_3 content was not greatly changed in soybean leaf but there was a great reduction of NO_3 in root by the flood stress. The growth characteristics of flooded plants also were reduced compared to the non-flooded plant at both stages. The seed yield, pod number and seed weight significantly reduced when the flood stress was applied at V4 to V5 and R2 stage. Specially, the yield reduction was more sensitive at R2 than V4 toV5 stage in Hannamkong. Furthermore, in this paper, the relationship between photosynthetic parameters and yield will be discussed.