Phosphorylation of chloroplast thylakoid membrane proteins, including LHC-II and PS II polypeptides D1, D2, CP43 and the psbH gene product, occurs under plastoquinone-reducing conditions. Dephosphorylation of LHC-II and PS II phosphoproteins proceeds under plastoquinone-oxidizing conditions, but with differing kinetics. This study shows that phosphorylation sites of PS II polypeptides are substrates for exogenous alkaline phosphatase activity, whereas those of LHC-II are not. By combined use of exogenous and endogenous phosphatase activities four types of thylakoid membrane are generated, with (i) both LHC-II and PS II polypeptides phosphorylated, (ii) only PS II polypeptides phosphorylated, (iii) only LHC-II phosphorylated and (iv) neither class of polypeptide phosphorylated. Examination of PS II electron transport in each membrane type shows that a mechanism involving phosphorylation of PS 11 polypeptides specifically is required for PS II function at high light intensity. Phosphorylation of LHC-II results in an inhibition of PS II electron transport at limiting light intensity which can therefore be attributed to decreased PS II absorption cross-section. Q(B) binding is unaffected by phosphorylation in any membrane type, nor are changes in function at the donor side of PS II involved. The role of PS II polypeptide phosphorylation in energy dissipation and protection from photoinhibition is discussed.