Incubation of isolated chloroplast thylakoid membranes with [gamma-32P]ATP results in phosphorylation of surface-exposed segments of several membrane proteins. The incorporation of 32P is light dependent, is blocked by 3(3,4-dichlorophenyl)-1,1-dimethylurea (diuron, an inhibitor of electron transport), but is insensitive to uncouplers of photophosphorylation. Polypeptides of the light-harvesting chlorophyll a/b-protein complex are the major phosphorylated membrane proteins. Addition of ATP to isolated chloroplast thylakoid membranes at 20 degrees C results in a time-dependent reduction of chlorophyll fluorescence emission; this is blocked by diuron but not by nigericin. ADP could not substitute for ATP. Chlorophyll fluorescence induction transients showed a decrease in the variable component after incubation of the membranes with ATP. Chlorophyll fluorescence at 77 K of phosphorylated thylakoid membranes showed an increase in long-wavelength emission compared with dephosphorylated controls. We conclude that a membrane-bound protein kinase can phosphorylate surface-exposed segments of the light-harvesting pigment-protein complex, altering the properties of its interaction with the two photosystems such that the distribution of absorbed excitation energy increasingly favors photosystem I.