One of the effective ways to address the effects of abnormal climate change on plant is to find germplasms that have better resistance to adverse environments. In this paper, we studied the responses of 5 pepper species Capsicum annuum L. (CA), C. baccatum L. (CB), C. chinense Jacquin. (CC), C. frutescens L. (CF) and C. pubescens Ruiz & Pavon (CP) as well as a wild pepper C. baccatum var. baccatum (CBY) to waterlogging stress. The results showed that warterlogging treatment greatly decreases photosynthetic pigment content, net photosynthetic rate (PN) and stomatal conductance (gs), and dramatically increases proline content and water-use efficiency (WUE) in all tested pepper, suggesting that pepper has weak resistance to waterlogging stress. The results also showed that changes of the above parameters vary in different species. CP had the smallest decreases in photosynthetic pigment content, PN, and gs and greatest increases in proline content and WUE. By contrast, CC had the greatest decreases in photosynthetic pigment content, P N, and gs and smallest increases in proline content and WUE, indicating that different species had different resistance to adverse environment and species CP and CC had the strongest and the weakest resistances, respectively. In addition, the study also demonstrated that wild pepper CBY had better resistance to adverse environment than all the tested species, indicating loss of the stress resistance genes during the process of domestication. Taking together, our study strongly suggests that pepper species should crossbreed with other species and wild pepper to expand genetic diversity, enlarge genetic distance, promote production, and improve the resistance to adverse environments. and L. J. Ou ... [et al.].