PsbZ (Ycf9) is a membrane protein of PSII complexes and is highly conserved from cyanobacteria to plants. We deleted the psbZ gene in the thermophilic cyanobacterium, Thermosynechococcus elongatus. The mutant cells showed photoautotrophic growth indistinguishable from that of the wild type under low and standard light conditions, while they showed even better growth than the wild type under high light. The mutant accumulated less carotenoids and more phycobiliproteins than the wild type under high light, suggestive of tolerance to photoinhibition. The mutant cells evolved oxygen at a rate comparable with the wild type, while the PSII complex isolated from the mutant retained much lower activity than the wild type. N-terminal sequencing revealed that Ycf12 and PsbK proteins were almost lost in the PSII complex. These results indicate that PsbZ is involved in functional integrity of the PSII complex by stabilizing PsbK and Ycf12. We suggest that Ycf12 is an unidentified membrane-spanning polypeptide that is placed near PsbZ and PsbK in the crystal structure of PSII.