Chloroplasts are the site of photosynthesis in green algae and land plants. This organelle derived from a single endosymbiotic event, in which a eukaryotic host cell engulfed a cyanobacterial ancestor. During organellogenesis, an extensive relocation of genetic material to the host nucleus occurred. Consequently, photosynthetic processes in the chloroplast demand a tight coordination of gene expression in two genetic compartments, and the proper assembly and function of genetically-chimeric multi-protein complexes. The evolution of photosynthetic eukaryotes created novel nuclear encoded proteins to sustain a stable fusion of the two organisms. Concomitantly, nuclear encoded proteins evolved with functions in the regulation of photosynthesis allowing the adaptation of photosynthetic eukaryotes to multiple environmental conditions and acclimation to changes within. In the scope of this review, different approaches for identifying novel photosynthesis-associated proteins are described. Additionally, the current state of the molecular dissection of selected chloroplast processes will be discussed with focus on the effect of phosphorylation events on the regulation of photosynthesis in response to changes in incident light.