Abstract: The paper aims to promote the breeding of waterlogging resistant pepper varieties, and to solve the flooding problems of pepper in the production，to study the effects of flooding stress on the physiological and biochemical characteristics of pepper seeds, and to provide a theoretical basis for the breeding of waterlogging resistant pepper varieties. In this paper the author studied three hot pepper species ‘S15’, ‘A46’ and ‘A77’, which waterlogging sensitivity is low, medium and high in production. Their seeds were under waterlogging respectively for 0 h, 10 h, 5 d, 10 d, 15 d and 20 d. The investigations were carried out on the changes of SOD, POD, CAT and GR activities, proline and soluble sugar contents, superoxide anion and hydroxyl radical contents of the three, and their germination potential and germination rate after different waterlogging stress were also studied. The study found that different waterlogging sensitivity pepper seeds had different response to waterlogging. In the case of severe waterlogging stress, ‘S15’ had the lowest hydroxyl radical and superoxide anion content, the highest content of Pro and soluble sugar and the highest glutathione reductase activity. ‘A77’ had the lowest soluble sugar content, the lowest activity of SOD and CAT, but highest hydroxyl radical content. Waterlogging treatment for 5 days could be used as the best time for waterlogging identification of simulated flood stress. After comprehensive evaluation, different pepper seeds showed the same waterlogging resistance with the actual. The correlation analysis of physiological and biochemical indexes showed that there were no remarkable correlation between each index; all indexes could be used to evaluate the resistance of cultivars under waterlogging stress.