Oxygenic photosynthesis evolved in the thylakoid membrane of ancient cyanobacteria. Here we review, from the proteomics viewpoint, the composition and biogenesis of the present day cyanobacteria thylakoid membranes, with main emphasis on the macromolecular protein complexes involved in photosynthetic electron transfer. Response of the thylakoid membrane proteome to changes in environmental cues and to various stress conditions is also described and discussed in terms of dynamic modifications in metabolic and catabolic pathways in order to adjust cyanobacterial cells to a new environment.