Increased human activities have had a significant impact on the global climate. Abnormal changes, such as drought stress caused by long-term un-rain, can affect plant growth and development. Pepper (Solanaceae), originally planted in tropical areas of South America, not only has medicinal value it has the highest vitamin C content of all vegetables. The International Board for Plant Genetic Resources (IBPGR) has classified pepper species into five species: Capsicum annuum L. (CA), Capsicum baccatum L. (CB), Capsicum chinense Jacquin. (CC), Capsicum frutescens L.(CF), Capsicum pubescens Ruiz and Pavon (CP). CA is the most differentiated, widely cultivated species being the focus of pepper breeding worldwide. Screening of resistant germplasms is one of the most important measures against abnormal climate changes. Pot experiments were employed to determine the photosynthetic response and associated physiological characters, such as superoxide dismutase (SOD) and glutathione reductase (GR) activities, root activity and adventitious root number, of five domesticated and one wild pepper species (C. baccatum var. baccatum (CBY)) to drought stress. The photosynthetic pigment content decreased the net photosynthetic rate (P_N) of all tested peppers continued to decline on the first day of regular irrigation, then started to increase on the second day, and almost recovered to normal levels by the seventh day. Non-photochemical quenching (qN), water use efficiency (WUE), and root activity had increased dramatically, the SOD and GR activities of all the pepper species first increased, being highest on day 4, and subsequently decreased. The number of adventitious roots slightly increased in all peppers, suggesting that pepper has a stronger resistance to drought stress. The results also show that changes in the above parameters vary in different species. CB had smaller decreases in photosynthetic pigment content, P_N, and stomatal conductance (g_s), and greater increases in qN, WUE, SOD and GR activities and root activity, indicating that CB has the strongest resistance to drought stress. CC and CF showed bigger decreases in photosynthetic pigment content, P_N, and g_s, with smaller increases in qN, WUE, SOD, and GR activities and root activity, indicating they have weaker drought stress resistance. In addition, the wild pepper, C. baccatum var. baccatum (CBY), had the smallest decrease in photosynthetic pigment content, P_N, and g_s, with the greatest increases in qN, WUE, SOD, and GR activities, and root activity. This indicates that CBY has better resistance to adverse environments than all tested species, which is perhaps caused by the loss of stress resistance genes during the process of domestication. Our study found that, of the species tested, the ability to resist drought stress is strongest in wild pepper CBY. Of the five species tested, CB had the highest photosynthetic rate and strongest drought resistance capability. In conclusion, we suggest that crossbreeding of domestic and wild pepper species be considered for commercial breeding. Such a measure will not only expand the genetic pool, increasing genetic distance and eventually increasing production; it will also to introduce elite stress tolerance genes improving each species' ability to resist adverse environments.