The D1 protein subunit of the photochemical reaction center II (RCII) turns over rapidly in oxygenic photosynthetic organisms exposed to the light. At high photon flux densities (PFD), photoinactivation of RCII precedes the degradation of the D1 protein. We found that the apparent quantum yield for the D1 protein degradation in Chlamydomonas cells is severalfold higher at low PFDs (10-100 μmol m-2 s-1) as compared to that observed at PFDs which induce photoinactivation of RCII (1.5-3 × 103 μmol m-2 s-1). Relative high levels of reduced RCII secondary plastoquinone acceptor, Q-B, are induced in cells exposed to low PFDs as determined by thermoluminescence measurements. The probability of generating elevated levels of Q-B which may recombine with the S2,3 oxidized states of the oxygen evolving complex decreases with increase in the light intensities at which consecutive double reduction of QB and exchange with the plastoquinone pool prevail. We have used light flashes to test if a correlation exists between the degradation of D1 protein and the relative level of Q-B. D1 protein degradation could be induced in dark-incubated cells exposed to a series of 1.4 × 103 single light flashes given at intervals compatible with generation of elevated levels of Q-B and its decay by charge recombination. Oscillations of the Q-B level in cells exposed to 960-1440 series of 1 to several flashes correlated with oscillations of the D1 protein degradation in Chlamydomonas cells and in the Scenedesmus wild type but not in the LF-1 mutant lacking photosystem II donor side activity. In this mutant the "S state cycle" and Q-B oscillations are abolished. We propose that the process of recombination of long lived RCII-Q-B with the S2,3 states may involve damaging events related to the D1 protein degradation induced by light flashes or continuous low light in vivo.