Thylakoid membranes carry out photosynthetic electron transport using some of the most sophisticated macromolecular multisubunit complexes in nature. Recent years have seen major breakthroughs in elucidating the ultrastructure of all core constituents of these complexes, i.e., photosystem II (PSII), the cytb6f complex and photosystem I (PS I) (Eberhard et al., 2008; Umena et al., 2011). They are composed of dozens of protein subunits as well as hundreds of organic and inorganic co-factors, most of which are embedded in the lipid bilayer of thylakoid membranes. Despite this profound knowledge on the architecture and function of the thylakoid membrane relatively little is known about how and where these complexes are assembled during thylakoid membrane biogenesis. In general, the biogenesis process includes the highly-ordered, step-wise assembly of proteins, lipids, pigments like chlorophyll (Chl), and carotenoids, quinones, and metal ions which to a large extent is mediated by dedicated assembly factors assisting specific steps (Schottler et al., 2011; Komenda et al., 2012; Nickelsen and Rengstl, 2013). Thus, fundamental questions discussed here concern the pathways and their cytological organization, by which these proteins as well as their co-factors are synthesized and assembled. How are these processes coordinated in time and space? Recently, analyses of thylakoid membrane biogenesis in both cyanobacteria and green algae have provided the first evidence for specialized membranous compartments which are distinct from functional thylakoid membranes but involved in the synthesis and assembly of at least some photosynthetic components, especially PSII. These findings have occurred amidst an era of modern bacterial cell biology in which advances in the resolution of fluorescence microscopy are being used to reveal an astonishingly high degree of compartmentalization of diverse processes in gram negative bacteria (Montero Llopis et al., 2010; Govindarajan et al., 2012). Here, we summarize our current knowledge and outline open questions on the degrees to which pathways that synthesize and assemble thylakoid membrane complexes and the lipid bilayer occur in specialized biogenic compartments in cyanobacteria and chloroplasts.