The effects of benzoquinone analogues, phenyl-1,4-benzoquinone (PBQ) and 2,5-dibromo-3-methyl-6-isopropyl-1,4-benzoquinone (DBMIB), on state transitions in Synechocystis sp. PCC 6803 were investigated. PBQ induced a transition from state 2 to state 1 in the absence of actinic light whereas DBMIB caused a state 2 transition. 3-(3,4-Dichlorophenyl)-1,1-dimethyl urea could not eliminate the effects of PBQ and DBMIB. These results imply that the redox state of the plastoquinone pool controls the state transitions in vivo and cytochrome b6f complex is involved in this process. As a working hypothesis, we propose that the occupancy of the quinol oxidation site and the movement of the Rieske protein may be pivotal in this regulation.