Light energy absorbed by the chloroplast membranes of higher plants is dissipated by nonradiative de-excitation in order to protect against photodamage. In photosystem II, which is the photosynthetic component most sensitive to photoinhibition, three pigment binding subunits, called CP24, CP26, and CP29, have been proposed to act in the regulation of the chlorophyll excited states concentration. In heavy stress conditions, CP29 becomes phosphorylated in its stroma-exposed portion, and this process is reversed by returning to normal conditions. In this study, we have used the pigments bound to the intramembrane hydrophobic portion of the protein as intrinsic probes to detect conformational changes induced by phosphorylation. We isolated the phosphorylated and unphosphorylated forms of the protein and showed that, although they have the same pigment complement, spectral differences can be consistently detected by absorption, linear dichroism, and circular dichroism spectroscopy. Alkaline phosphatase treatment of the phosphoprotein restores both the electrophoretic mobility and the spectral properties of the unphosphorylated CP29. The results of this study show that phosphorylation of CP29 can modulate the spectral properties of this photosystem II subunit and provide a possible mechanism for the regulation of excitation energy supply to the reaction center.