Non-photochemical redox changes of the plastoquinone pools in darkness were investigated in the cyanobacterium Synechocystis sp. PCC 6803 by monitoring changes in Chl fluorescence yield during light-to-dark transitions. The inhibitors rotenone and mercury with or without 1 mM succinate fully suppressed the post-illumination increase in Chl fluorescence in both NADPH dehydrogenase-defective (M55) and deltaCtaI cells. The latter cells lack subunit I of cytochrome aa3-type cytochrome c oxidase. These results strongly suggest that NADPH dehydrogenase plays the major role in electron donation in the non-photo-chemical reduction of plastoquinone. The rising phase of post-illumination Chl fluorescence in both wild type pretreated with KCN, and deltaCtaI cells, was significantly slowed by low light illumination. We detected comparable photochemical levels of both photosystem (PS) II and PSI during steady state illumination in wild type and deltaCtaI cells. From these results, we suggest that respiratory electron flow involved in the non-photochemical redox change of plastoquinone is not likely to occur in the light.