Redox-dependent thylakoid protein phosphorylation regulates both short- and long-term acclimation of the photosynthetic apparatus to changes in environmental conditions. The major thylakoid phosphoproteins belong to photosystem (PS)II (D1, D2, CP43, PsbH) and its lightharvesting antenna (Lhcb1, Lhcb2, CP29) but a number of minor phosphoproteins have also been identified. The detection methods traditionally include the radiolabeling techniques, electrophoretic separation of the phosphorylated and unphosphorylated forms of the protein, and the use of phosphoamino acid antibodies. The recent progress in mass spectrometry (MS) techniques and methods of proteomics allow for successful identification and analyses of protein phosphorylation. In mass spectrometry approaches, exogenous tracer is not needed and natural phosphorylation of proteins can be characterized with high sensitivity yielding the mapping of exact phosphorylation sites in the proteins as well. Various methods for detection of thylakoid phosphoproteins, including the preparation of phosphopeptides for mass spectrometric analyses and techniques for phosphopeptide identification by electrospray ionization MS are described. The experimental protocols for simultaneous identification of multiple phosphopeptides in complex peptide mixtures and for assess of stoichiometry for in vivo phosphorylation of multiple proteins are outlined.