To elucidate the protective mechanisms against photodamage in photosynthetic apparatus of rice, the difference in traits related to xanthophyll cycle, chlorophyll fluorescence and photosynthetic CO2 exchange among indica japonica hybrids and their parents under midday strong light were studied. Obviously diurnal variation of apparent quantum yield (AQY), D1 protein content, ratio of photorespiration/photosynthesis (Pr/Pn), PS Ⅱ photochemical efficiency (Fv/Fm),non photochemical quenching (qN) and xanthophyll cycle[content of violaxanthin(V), antheraxanthin(A), and zeaxanthin(Z)]in leaves of different genotype rice were observed. Japonica rice kept higher D1 protein content, Fv/Fm and AQY, but lower level of (A+Z)/(A+Z+V), Pr/Pn and qN, as compared with indica rice. However, the physiological parameters mentioned above in reciprocal cross F1 hybrids were between those of their parents, but closed to their maternal lines. The lower AQY and Fv/Fm and higher (A+Z)/(A+Z+V) and Pr/Pn in indica/japonica F1 hybrids than in japonica/indica F1 hybrids were depended on different source of their plastid genes. Data processing showed that markedly positive correlation between D1 protein content and Fv/Fm or AQY and negative correlation between D1 protein content and (A+Z)/(A+Z+V),Pr/Pn or qN were presented. Besides, a positive correlation between (A+Z)/(A+Z+V) and qN was also observed. Furthermore, there was less zeaxanthin content and , as a result, more net loss of D1 protein in the leaves treated with dithiothretol (DTT) than those in control leaves under midday strong light. According to these results, the levels and stabilities of D1 protein encoded by plastid gene from maternal line were proposed as the main physiological basis of the difference in characteristics related to xanthophyll cycle, chlorophyll fluorescence and photosynthetic CO 2 exchange among different genotypes of rice, and the xanthophyll cycle in leaves played an important role in protecting photosynthetic apparatus against photodamage.