Abstract Acclimation of Photosynthesis to Environment 1 (APE1) has been identified as a protein involved in the adaptation of plants to high illumination. Several studies indicate its association with photosystem II (PSII), but its specific function in photosynthesis has not yet been determined. In this study, we used biochemical and molecular biology approaches to identify the function of APE1 in Arabidopsis (Arabidopsis thaliana) and the cyanobacterium Synechocystis sp. PCC 6803. APE1 elimination in the plant altered various, seemingly unrelated, photosynthetic processes, such as maximum quantum efficiency of PSII, non-photochemical quenching (NPQ), and state transitions. The levels of PSII core proteins were reduced in the ape1 mutant. Our results indicated that APE1 is involved in the formation or stabilization of the RC47 complex of PSII, in both plants and cyanobacteria. The alterations in NPQ and state transitions of the plant were a consequence of the lesion in PSII. These alterations were observed only when the mutant was stressed by high-light treatment, confirming that APE1 is necessary for optimal PSII performance under high-light stress.