The influence of submergence on photosynthesis and antioxidant capacities in rice varieties Swarna and Swarna-Sub1 with or without Sub1 QTL were evaluated under control,simulated complete submergence and subsequent re-aeration.The leaf photosynthetic rate and stomatal conductance decreased in the both varieties during the progression of submergence as compared to the control plants,but significant varietal differences were observed after 1 d of submergence.Submergence also altered the PSII activity,as reflected in a decrease in the values of Fo,Fm and Fv/Fm and degradation of chlorophyll,more in Swarna than in Swarna-Sub1.During early submergence period,the activities of superoxide dismutase(SOD),ascorbate peroxidase(APX),dehydroascorbate reductase(DHAR),glutathione reductase(GR) against reactive oxygen species were increased in the both varieties.However,with the progress of submergence period(after 7 d),the activities of SOD,catalase(CAT),APX,guaiacol peroxidase(GPX),GR and DHAR declined,more in Swarna than in Swarna-Sub1.During re-aeration,Swarna-Sub1 showed significant increase of above antioxidant enzymes but not in Swarna.Swarna-Sub1 improves photosynthetic activity,showing higher photosynthetic rate compared to Swarna under submergence and subsequent re-aeration because of less degradation of chlorophyll,higher stomatal conductance,and efficient PSII activity along with better antioxidant protection from oxidative damage. The influence of submergence on photosynthesis and antioxidant capacities in rice varieties Swarna and Swarna-Sub1 with or without Sub1 QTL were evaluated under control, simulated complete submergence and subsequent re-aeration. The leaf photosynthetic rate and stomatal conductance decreased in the both species during the progression of submergence as compared to the control plants, but significant varietal differences were observed after 1 d of submergence. Submergence also altered the PSII activity, as reflected in a decrease in the values ​​of Fo, Fm and Fv / Fm and degradation of chlorophyll, more in Swarna than in Swarna-Sub. Early early submergence period, the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), dehydroascorbate reductase (DHAR), glutathione reductase (GR) against reactive oxygen species were increased in the both varieties . With, the progress of submergence period (after 7 d), the activities of SOD, catalase (CAT), APX, guaiacol peroxidase (GPX), GR and DHAR decl ined, more in Swarna than in Swarna-Sub1.During re-aeration, Swarna-Sub1 showed significant increase of above antioxidant enzymes but not in Swarna. Warna-Sub1 improves photosynthetic activity, showing higher photosynthetic rate compared to Swarna under submergence and subsequent re -aeration because of less degradation of chlorophyll, higher stomatal conductance, and efficient PSII activity along with better antioxidant protection from oxidative damage.