Pepper (Capsicum sp.) is one of the major vegetable crops in the world. Recently, flooding frequently occurs around the world as climatic change becomes more serious. Especially, damages of flooded pepper continuously increased in poorly drained cultivation areas and paddy upland soil of pepper. This experiment was carried out to investigate the flooding stress tolerance of pepper accessions among the World Vegetable Center collection during the summer growing season. We used 17 pepper accessions from five species, (C. annuum; C. baccatum; C. chacoense; C. Chinese, and C. frutescens) and grew the seedlings for two months in seven-inch pots filled with sterilized garden soil with four replications. After the two-month growth, flooding was imposed for five days by submerging the pots into water. Growth and stress responses were measured to evaluate tolerance to flooding stress of the accessions. Five days after the flooding treatment, the pots were drained and maintained for three days for recovery. Finally, three days after the water drainage, growth and stress responses were reevaluated to assess plant recovery from flooding stress. After five days of flooding, plant height decreased with the exceptions of PBC2029, VI028788, VI029116, VI057807, VI029485, and PBC 934, which were not significantly different from the control. Plant canopy width was significantly depressed by the flooding for all accessions. The number of flowering plants tended to be decreased by the flooding treatment but there was no significant difference. In the summer season, wilting quickly occurred all of the accessions; especially, C. chinense and C. frutescens accessions were sensitive to flooding stress but AVPP9824 (C. annuum), VI029119, and VI044312 (C. chacoense) showed resistant response to the flooding. In all flooded accessions, the leaf temperature of pepper significantly increased at five days compared to the first day of flooding. SPAD index of pepper tended to be decreased in most accessions but, AVPP9824 and VI013286 were not different compared to the control. Pollen viability was variable among the accessions of this experiment. Proline content significantly increased in all of the accessions by the flooding treatment. From the results, we found that AVPP9824 (C. annuum), VI029119, and VI044312 (C. chacoense) accessions exhibited tolerance characteristics to flooding stress in the measured variables, but further research is needed to confirm this finding.