The PsbS subunit of photosystem II (PSII) plays a key role in nonphotochemical quenching (NPQ), the major photoprotective regulatory mechanism in higher plant thylakoid membranes, but its mechanism of action is unknown. Here we describe direct evidence that PsbS controls the organization of PSII and its light harvesting system (LHCII). The changes in chlorophyll fluorescence amplitude associated with the Mg 2؉ -dependent restacking of thylakoid membranes were measured in thylakoids prepared from wild-type plants, a PsbS-deficient mutant and a PsbS overexpresser. The Mg 2؉ requirement and sigmoidicity of the titration curves for the fluorescence rise were negatively correlated with the level of PsbS. Using a range of PsbS mutants, this effect of PsbS was shown not to depend upon its efficacy in controlling NPQ, but to be related only to protein concentration. Electron microscopy and fluorescence spectroscopy showed that this effect was because of enhancement of the Mg 2؉ -dependent re-association of PSII and LHCII by PsbS, rather than an effect on stacking per se. In the presence of PsbS the LHCII⅐PSII complex was also more readily removed from thylakoid membranes by detergent, and the level of PsbS protein correlated with the amplitude of the psi-type CD signal originating from features of LHCII⅐PSII organization. It is proposed that PsbS regulates the interaction between LHCII and PSII in the grana membranes, explaining how it acts as a pH-dependent trigger of the conformational changes within the PSII light harvesting system that result in NPQ.Light harvesting antennae in plant photosynthesis increase the rate at which absorbed photons excite the photosynthetic reaction centers. In the case of photosystem II (PSII) 3 in higher plants, light harvesting is carried out by a complex assembly of chlorophyll protein antenna complexes (LHCII) located in the grana membranes of the chloroplast (1). The main components are trimeric LHCIIb and monomeric CP24, CP26, and CP29. These are associated together with the dimeric PSII reaction center core complexes to form LHCII⅐PSII supercomplexes (2). The minimal unit of the supercomplex comprises two cores (C 2 ) and two strongly bound LHCIIb trimers (S 2 ), together with two copies of CP26 and CP29, referred to as the C 2 S 2 LHCII⅐PSII supercomplex (3). Two further trimers bound with moderate strength (M 2 ) together with CP24 make up the most predominant supercomplex, C 2 S 2 M 2 . LHCII⅐PSII supercomplexes are segregated from photosystem I, associating together in the lateral plane of the thylakoid membrane, sometimes forming highly ordered semi-crystalline domains. Transverse associations between the outer stromal surfaces of these proteins result in membrane appression and the characteristic grana stack. Although this highly conserved macro-organization of the PSII antenna has been rationalized in terms of efficient capture and utilization of light (4), it can be argued that it is the enabled structural and functional flexibility that is probably more important. Changes ...