Cyanobacteria are omnipresent photosynthetic microorganisms that are crucial for the proper functioning of multiple environmental niches. Recently, these organisms have found various applications in soil remediation, waste utilization, and the production of biodegradable polymers. A significant volume of the cyanobacterial cell is occupied by thylakoid membranes, where the photosynthesis process is localized. These membranes are inhomogeneous and highly compartmentalized; however, the stimuli and forces leading to such a high degree of self-organization are not entirely understood. In our study, we apply Langmuir monolayers formed by the main lipids of cyanobacterial membranes: monogalactosyldiacylglycerol (MGDG), digalactosyldiacylglycerol (DGDG), sulfoquinovosyldiacylglycerol (SQDG), and phosphatidylglycerol (PG), as versatile models of thylakoid membranes. Special attention was paid to the binary system formed by the two neutral glycolipids MGDG and DGDG, as these two substances are most abundant in the membrane. Then the effects implied by the incorporation of anionic lipids were investigated. The morphology of the monolayers was studied by Brewster angle microscopy, while the ordering of the monolayer-forming molecules on the molecular scale was investigated with the Grazing incidence X-ray diffraction technique. It was proved that the inhomogeneous structure of cyanobacterial membrane is an intrinsic property of the applied structural lipids. It was also proved that the increase in anionic lipid content, frequently applied by cyanobacteria as a response to unfavorable environmental conditions, leads to significant changes in the morphology of the model membranes.