Photosystem II (PSII) is a multiple-subunit membrane complex found in cyanobacteria and chloroplasts, which acts as a light-driven water-plastoquinone oxidoreductase. Although the functionality and structure of PSII are well understood, its assembly and repair mechanisms are still not fully comprehended. This study employs cryogenic electron microscopy (cryo-EM) to investigate the PSII assembly and repair processes. In Chapter 3, we determined a cryo-EM structure of Ycf48/RCII/PSI assembly complex from Synechocystis sp. PCC 6803. This complex has an accessory factor protein Ycf48 bound to the luminal side of RCII, which is a sub-complex of PSII involved in the early stage of PSII assembly. A cluster of conserved arginine residues, named the Arg patch, of Ycf48 interacts with RCII, preventing premature formation of the fully functional PSII complex. In Chapter 4, we successfully purified an RCII sub-complex from Synechocystis sp. PCC 6803 with more accessary factors through Flag pull-downs. Although homogeneous RCII sub-complexes for cryo-EM analysis were not obtained, these Flag pull-downs facilitate the purification of the early-stage PSII sub-complexes. During the purification of Thermosynechoccus elongatus PSII, four fractions were obtained at the ion exchange chromatography, with the fourth fraction, named Peak 4, remaining elusive. In Chapter 5, we determined the structure of complexes from Thermosynechoccus elongatus Peak 4 PSII, which is found to be composed of active (2 active), semi-active (active + inactive) and inactive (2 inactive) PSII dimers. These dimeric Peak 4 PSII complexes could be either the final-stage assembly or early-stage disassembly PSII intermediates. In the case of assembly PSII, we proposed that the folding of the C-terminal tail of D1 induces the final stage of PSII assembly. In the other case, the oxidation of PSII residues at the donor side likely triggers the disassembly of PSII. In Chapter 6, Synechocystis sp. PCC 6803 FtsH2/FtsH3 hetero-hexamer protease, which selectively degrades damaged PSII proteins during PSII repair, was successfully purified through Flag pull-down. However, the FtsH proteins likely underwent self-degradation during purification, preventing the acquisition of a homogeneous sample for cryo-EM analysis. Overall, this study provides new insights into the mechanism of PSII assembly and highlights the power of cryo-EM in elucidating protein complex structures.