Thylakoid membranes are indispensable parts of chloroplasts and other cyanobacterial cells. They are a separate membrane system, manifesting as closed vesicles (sacks), separated from the chloroplast envelope or cyanobacterial plasma membrane. They host photosynthetic processes and provide a unique environment for their optimal performance. The first important advantage of thylakoid’s presence is high photosynthetically active area, packed in relatively small space of chloroplasts. Thylakoids composition, concerning lipids, proteins, and pigments makes them a unique type of membrane, with high structural and functional conservation upon evolution. In this Chapter, we describe processes that lead to the formation of thylakoid architecture in both chloroplasts (especially of angiosperm) and cyanobacterial cells. We also discuss how the architecture is maintained and tuned upon varying environmental conditions, and how the thylakoid disassembly, which occurs during senescence or transformation to another type of plastid, is governed.