The structural changes associated to non-photochemical quenching in cyanobacteria is still a matter of discussion. The role of phycobilisome and/or photosystem mobility in this mechanism is a point of interest to be elucidated. Changes in photosystem II fluorescence induced by different quality of illumination (state transitions) or by strong light were characterized at different temperatures in wild-type and mutant cells, that lacked polyunsaturated fatty acids, of the cyanobacterium Synechocystis PCC 6803. The amplitude and the rate of state transitions decreased by lowering temperature in both strains. Our results support the hypothesis that a movement of membrane complexes and/or changes in the oligomerization state of these complexes are involved in the mechanism of state transitions. The quenching induced by strong blue light which was not associated to D1 damage and photoinhibition, did not depend on temperature or on the membrane state. Thus, the mechanism involved in the formation of this type of quenching seems to be unrelated to the movement of membrane complexes. Our results strongly support the idea that the mechanism involved in the fluorescence quenching induced by light 2 is different from that involved in strong blue light induced quenching.