The oxygen-evolving photosystem II (PSII) complex located in chloroplasts and cyanobacteria is sensitive to light-induced damage 1 which unless repaired causes reduction in photosynthetic capacity and growth. Although a potential target for crop improvement, the mechanism of PSII repair remains unclear. The D1 reaction center protein is the main target for photodamage 2 , with repair involving the selective degradation of the damaged protein by FtsH protease 3 . How a single damaged PSII subunit is recognised for replacement is unknown. Here, we have tested dark stability of PSII subunits in strains of the cyanobacterium Synechocystis PCC 6803 blocked at specific stages of assembly. We have found that when D1, which is normally shielded by the CP43 subunit, becomes exposed in a photochemically active PSII complex lacking CP43, it is selectively degraded by FtsH even in the dark. Removal of the CP47 subunit, which increases accessibility of FtsH to the D2 subunit, induced dark degradation of D2 at a faster rate than that of D1. In contrast CP47 and CP43 are resistant to degradation in the dark. Our results indicate that protease accessibility induced by PSII disassembly is an important determinant in the selection of the D1 and D2 subunits to be degraded by FtsH. 3The unusually high rate of synthesis and degradation, or turnover, of the D1 subunit of PSII, first observed over 40 years ago 4,5 , reflects the selective replacement of D1 during the repair of PSII in response to light damage. In the cyanobacterium Synechocystis sp. PCC 6803 (hereafter referred to as Synechocystis), degradation of D1 is mediated by a specific membrane-bound FtsH2/FtsH3 protease complex 3 . How FtsH complexes differentiate between damaged and undamaged D1 subunits is unclear 6 . Given that the D1 protein is shielded in PSII by the PSII inner antenna, CP43, several small transmembrane PSII subunits as well as extrinsic proteins on the lumenal side of the complex, one possibility is that at least partial disassembly of PSII, possibly triggered by photodamage, facilitates contacts between FtsH and D1. If selective degradation of D1 is primarily driven by accessibility, which does not need to be caused just by photo-oxidative damage to D1, one interesting prediction is that undamaged D1 might be preferentially degraded in the dark in PSII complexes that have been mutated to improve access.High resolution structures of cyanobacterial PSII have confirmed that the D1 and D2 reaction center subunits are shielded in the membrane by the intrinsic CP43 and CP47 subunits, and capped on the lumenal side of the membrane by three extrinsic subunits: PsbO, PsbU and PsbV (Fig. 1a) 7,8 . Synechocystis strains lacking the PsbO subunit still assemble oxygen-evolving PSII complexes but show a higher rate of D1 turnover than WT, possibly in response to an increase in the rate of photodamage to D1 due to perturbations on the donor side of PSII 9,10 . Enhanced D1 degradation in ΔPsbO might also be due to exposure of specific lumenal regions of D1 (normally hi...