Two sesame accessions, ZZM2541 and Ezhi-2, with different tolerance to waterlogging were selected, and the seedlings at the 4-true leaf stage were treated by waterlogging for 48 h. Growth parameters were evaluated 1 d before the beginning of waterlogging and on the 3~(rd)day after the removal of waterlogging(DARW). Morphological characteristics of root and chlorophyll fuorescence were measured on the 3~(rd)DARW and leaf gas exchange was measured on the zero, 3~(rd)and 15~(th) DARW. Results showed that sesame accessions ZZM2541 and Ezhi-2 responded to waterlogging in considerably different performance. The stress induced leaf chlorosis and abscission and slowed growth of plant height in both accessions, but symptom occurred seriously in the susceptive Ezhi-2. In the more tolerant ZZM2541, plentiful of adventitious roots formed above the level.All of the average values of maximum fuorescence yield(F_m), quantum efficiency of open PSII centres(F_v/F_m), initial fluorescence(F_v/F_0) and chlorophyll content(Chl) decreased at the 4-true leaf stage in both accessions after suffering to the stress.The decreases of F_m, F_v/F_0 and Chl were more pronounced in Ezhi-2 than in ZZM2541. Less reductions of mean photosynthetic rate(Pn), transpiration rate(Tr), and stomatal conductance(gs) were observed in the leaves of waterlogged ZZM2541 than in waterlogged Ezhi-2(compared to controls), and the leaves of Ezhi-2 showed a higher water use efficiency(WUE) after the removal of waterlogging. Based on the results, it was concluded that the tolerance to waterlogging of ZZM2541 appears to depend on a combination of photosynthetic characteristics responses and morphological adaption. Two sesame accessions, ZZM2541 and Ezhi-2, with different tolerance to waterlogging were selected, and the seedlings at the 4-true leaf stage were treated by waterlogging for 48 h. Growth parameters were evaluated 1 d before the beginning of waterlogging and on the 3 ~ (rd) day after the removal of waterlogging (DARW). Morphological characteristics of root and chlorophyll fuorescence were measured on the 3 ~ (rd) DARW and leaf gas exchange was measured on the zero, 3 ~ (rd) and 15 ~ (th) DARW. Results showed that sesame accessions ZZM2541 and Ezhi-2 responded to waterlogging in considerably different performance. The stress induced leaf chlorosis and abscission and slowed growth of plant height in both accessions, but symptom occurred in the susceptive Ezhi-2 . The more tolerant ZZM2541, plentiful of adventitious roots formed above the level. All of the average values ​​of maximum fuorescence yield (F_m), quantum efficiency of open PSII centers (F_v / F_m), initial fluorescence (F_v / F_0) and c Less reductions of mean photosynthetic rate (Kl) than at 4-true leaf stage in both accessions after suffering to stress. The reduction of F_m, F_v / F_0 and Chl were more pronounced in Ezhi-2 than in ZZM2541. Pn), transpiration rate (Tr), and stomatal conductance (gs) were observed in the leaves of waterlogged ZZM2541 than in waterlogged Ezhi-2 (compared to controls), and the leaves of Ezhi-2 showed a higher water use efficiency After the removal of waterlogging. Based on the results, it was concluded that the tolerance to waterlogging of ZZM2541 appears to depend on a combination of photosynthetic characteristics responses and morphological adaptations.