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Quenching of excess excitation energy is necessary for the photoprotection of light-harvesting complexes. In cyanobacteria quenching of phycobilisomes is induced by orange carotenoid protein (OCP) which photoactivation occurs under high light conditions. This process leads to a decrease in the efficiency of energy transfer from the phycobilisomes (PBS) to chlorophyll and reduction of activity of photosystem PSII. Importance of OCP in photoprotection is generally accepted, although some cyanobacteria exist without that protein. Considering the fact that both photochemical and non-photochemical quenching have similar effects on quantum yield of PBS fluorescence, in vivo estimations of OCP efficiency are complicated and require alternative approach. As known cyanobacteria compensate nitrogen deficiency by degradation of PBS, thus reducing the effective absorption cross-section of PSII. In the present study we followed this process in order to compare effects of the reversible OCP-dependent quenching of PBS with a reduction of its size. Analyzing these relationships, we found that OCP-dependent quenching triggered by blue light involves less than 40% of all PBS. This observation indicates that under normal conditions efficiency of photoprotection is limited by OCP concentration which is probably lower than concentration of PBS.