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Waterlogging threatens severely to the sesame production in China, India and Burma, which are the top three sesame producers of the world.It was of great importance to explore the dynamics and mechanisms of action of anaerobic proteins and antioxidant enzymes together with the morph-anatomic adaptions in waterlogged sesame.The sesame accessions ZZM2541 and Ezhi-2 respond to waterlogging in considerably different performance.The stress induced wilting and leaf chlorosis in both accessions, but symptom occurred earlier in the susceptive Ezhi -2.In the more tolerant ZZM2541, adventitious roots formed above the flooding level, and plentiful of aerenchyma developed in the root and stem.However, it was discovered no apparent intercellular spaces existing in the spongy mesophyll in leaves of both accessions.The activities of ADH, PDC and LDH increased in roots of both accessions after suffering of the stress.The increase of ADH and PDC activity was more pronounced in ZZM2541, while a significantly higher LDH activity appeared in Ezhi-2.All the activities of SOD, APX and CAT were higher in the leaves of ZZM2541 than in Ezhi-2, and the leaves of Ezhi-2 showed a higher content of MDA throughout the duration of waterlogging.It was suggested that the tolerance to waterlogging of ZZM2541 appears to depend on a combination of metabolic and morpho-anatomical adaptions.