Pepper (Capsicum sp.) is a major vegetable crop that is widely cultivated around the world. As climatic change becomes more serious, flooding frequently occur in paddy upland soil and poorly drained cultivation area for growing pepper in Korea. The goal of this experiment was to identify flooding tolerant pepper accessions among the World Vegetable Center collection during the winter season. We used 19 pepper accessions from six species, (C. annuum; C. baccatum; C. chacoense; C. chinese; C. frutescens, and C. pubescens;) and grew the seedling for two months (three months for C. pubescens) in seven-inch pots filled with sterilized garden soil with five replications. Flooding was imposed for five days after and pots were drained and reevaluated eight days after the flooding experiment to assess plant recovery. After five days of flooding, plant height decreased with the exceptions of AVPP9824, VI029116, VI013286, VI057807, and VI037646, which were not significantly different from the control (no flooding). Plant canopy width was significantly depressed in the flooding for all of the C. pubescens accessions. In most accessions, number of flowering was decreased in the flooding treatment. Wilting did not occur quickly during the winter; however, three days after flooding the wilt index was severe for accessions of C. pubescens and C. chinense. After recovery, the wilt index of VI046870, AVPP9824, VI029116, VI012904, VI013286, VI029119, VI044312, VI044312, and VI029485 was below 2.5. Leaf temperature of most pepper increased at five days compared to the first day of flooding. SPAD index decreased in most accessions but, PBC 2029, VI029116, and VI044312 were not different from the control. Pollen viability was often reduced in the flooding treatment, but pollen viability of PBC 743, VI046870, VI029116, VI013286, VI029485, and PBC 934 was not significant from the non-flooded control. Proline content tended to increase in flooding treated plants and variability occurred among the accessions screened here. From the results, we found that C. pubescens accessions were typically sensitive to flooding stress, which is contradictory to previous reseach. C. annuum (VI046870, AVPP9824), C. baccatum (VI029116, VI012904, VI013286), C. chacoense (VI029119, VI044312, VI044312), and C. frutescens (VI029485) accessions could be tolerant to flooding, but further research is needed to confirm this.