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A prolonged (20 h) dark incubation of Chlorella pyrenoidosa algae at 37°C resulted in a twofold rise of the slowly rising phase (10–15 min), sFv, in the kinetics of variable chlorophyll fluorescence, Fv (Fv = Fm – F0) in diuron-treated cells. This effect suggests the accumulation of inactive photosystem II (PSII) complexes with low efficiency of primary quinone acceptor of electron of PSII (QA) reduction. The presence of methylamine (MA), a thylakoid membrane uncoupler, or N, N′-dicyclohexylcarbodiimide, an inhibitor of ATPase, precluded the accumulation of inactive PSII complexes. When salicylhydroxamate promoted the reduction of the plastoquinone (PQ) pool, exogenous ATP accelerated the accumulation of inactive complexes. Dark PQ oxidation in the presence of nonmetabolized glucose analog, 2-deoxy-D-glucose, lowered the content of inactive PSII complexes, and NaF, an inhibitor of chloroplast phosphatases, retarded this process. These data are considered as evidence for a mechanism regulating the content of inactive PSII complexes in the process of redox-dependent phosphorylation of D1- and/or D2-proteins of PSII.