The xanthophyll cycle and the water-water cycle had different functional significance in chilling-sensitive sweet pepper upon exposure to chilling temperature (4 °C) under low irradiance (100 µmol m-2 s-1) for 6 h. During chilling stress, effects of non-photochemical quenching (NPQ) on photosystem 2 (PS2) in dithiothreitol (DTT) fed leaves remained distinguishable from that of the water-water cycle in diethyldithiocarbamate (DDTC) fed leaves. In DTT-fed leaves, NPQ decreased greatly accompanied by visible inhibition of the de-epoxidized ratio of the xanthophyll cycle, and maximum photochemical efficiency of PS2 (Fv/Fm) decreased markedly. Thus the xanthophyll cycle-dependent NPQ could protect PS2 through energy dissipation under chilling stress. However, NPQ had a slighter effect on photosystem 1 (PS1) in DTT-fed leaves than in DDTC-fed leaves, whereas effects of the water-water cycle on PS1 remained distinguishable from that of NPQ. Inhibiting superoxide dismutase (SOD) activity increased the accumulation of O2, the oxidation level of P700 (P700+) decreased markedly relative to the control and DTT-fed leaves. Both Fv/Fm and NPQ changed little in DDTC-fed leaves accompanied by little change of (A+Z)/(V+A+Z). This is the active oxygen species inducing PS1 photoinhibition in sweet pepper. The water-water cycle can be interrupted easily at chilling temperature. We propose that during chilling stress under low irradiance, the xanthophyll cycle-dependent NPQ has the main function to protect PS2, whereas the water-water cycle is not only the pathway to dissipate energy but also the dominant factor causing PS1 chilling-sensitivity in sweet pepper. and X.-G. Li ... [et al.].