Illumination changes elicit modifications of thylakoid proteins and reorganization of the photosynthetic machinery. This involves, in the short term, phosphorylation of photosystem II (PSII) and light-harvesting (LHCII) proteins. PSII phosphorylation is thought to be relevant for PSII turnover 1,2 , whereas LHCII phosphorylation is associated with the relocation of LHCII and the redistribution of excitation energy (state transitions) between photosystems 3,4 . In the long term, imbalances in energy distribution between photosystems are counteracted by adjusting photosystem stoichiometry 5,6 . In the green alga Chlamydomonas and the plant Arabidopsis, state transitions require the orthologous protein kinases STT7 and STN7, respectively 7,8 . Here we show that in Arabidopsis a second protein kinase, STN8, is required for the quantitative phosphorylation of PSII core proteins. However, PSII activity under high-intensity light is affected only slightly in stn8 mutants, and D1 turnover is indistinguishable from the wild type, implying that reversible protein phosphorylation is not essential for PSII repair. Acclimation to changes in light quality is defective in stn7 but not in stn8 mutants, indicating that short-term and long-term photosynthetic adaptations are coupled. Therefore the phosphorylation of LHCII, or of an unknown substrate of STN7, is also crucial for the control of photosynthetic gene expression.STT7 and STN7 are orthologous protein kinases required for LHCII phosphorylation and for state transitions in Chlamydomonas and Arabidopsis, respectively 7,8 . In Arabidopsis, another STT7/STN7-like protein (STN8) exists that is not required for state transitions 8 . STN8 is located in the chloroplast, as shown by in vivo subcellular localization of its amino-terminal region fused to the dsRED protein and by the import of, and transit peptide removal from, STN8 translated in vitro (Fig. 1a, b). Chloroplast subfractionation after import revealed that the protein is associated, like STT7 and STN7, with thylakoids ( Fig. 1c) (refs 7, 8).Insertion mutants for STN8 and STN7 were obtained from the Salk collection 9 , and for each gene two independent mutant alleles lacking the respective transcript were identified (Supplementary Fig. S1). The stn7 stn8 double mutant was generated by crossing stn7 and stn8 single knockouts and screening the resulting F 2 generation for homozygous double mutants. All mutants were indistinguishable from the wild type with regard to the timing of seed germination and growth rate in the greenhouse ( Supplementary Fig. S1). In stn7 and stn7 stn8 mutants, a slight decrease in the levels of neoxanthin, lutein and total chlorophyll was found (Supplementary Table S1). These subtle changes can be attributed to a minor decrease in LHCII content, not detectable by polyacrylamide-gel electrophoresis (PAGE) analysis ( Supplementary Fig. S2).Photosynthetic electron flow, measured on the basis of chlorophyll fluorescence, was not altered in the mutants (Supplementary Table S2). State transitions w...