Cyanobacteria are photosynthetic microbes with highly differentiated membrane systems. These organisms contain an outer membrane, plasma membrane, and an internal system of thylakoid membranes where the photosynthetic and respiratory machinery are found. This existence of compartmentalization and differentiation of membrane systems poses a number of challenges for cyanobacterial cells in terms of organization and distribution of proteins to the correct membrane system. Proteomics studies have long sought to identify the components of the different membrane systems in cyanobacteria, and to date about 450 different proteins have been attributed to either the plasma membrane or thylakoid membrane. Given the complexity of these membranes, many more proteins remain to be identified, and a comprehensive catalogue of plasma membrane and thylakoid membrane proteins is needed. Here we describe the identification of 635 differentially localized proteins in Synechocystis sp. PCC 6803 by quantitative iTRAQ isobaric labeling; of these, 459 proteins were localized to the plasma membrane and 176 were localized to the thylakoid membrane. Surprisingly, we found over 2.5 times the number of unique proteins identified in the plasma membrane compared with the thylakoid membrane. This suggests that the protein composition of the thylakoid membrane is more homogeneous than the plasma membrane, consistent with the role of the plasma membrane in diverse cellular processes including protein trafficking and nutrient import, compared with a more specialized role for the thylakoid membrane in cellular energetics. Thus, our data clearly define the two membrane systems with distinct functions. Overall, the protein compositions of the Synechocystis 6803 plasma membrane and thylakoid membrane are quite similar to that of the plasma membrane of Escherichia coli and thylakoid membrane of Arabidopsis chloroplasts, respectively. Synechocystis 6803 can therefore be described as a Gram-negative bacterium with an additional internal membrane system that fulfills the energetic requirements of the cell. Photosynthetic microbes such as the cyanobacterium Synechocystis sp. PCC 6803 convert light to cellular energy, an ability that makes these organisms of particular interest in renewable energy studies. Cyanobacteria typically have a Gram-negative-type cell envelope consisting of a plasma membrane (PM) 1 , peptidoglycan layer, and outer membrane. These microbes also have an internal thylakoid membrane (TM) system where the protein complexes of the photosynthetic and respiratory electron transfer chains function. The presence of these differentiated membrane systems makes cyanobacteria more complex than other Gram-negative bacteria. There is considerable interest in understanding the roles of the membrane systems and their relation with each other. Our studies using electron tomography revealed that the TM in the cyanobacterium Cyanothece sp. ATCC 51142 forms a complicated network of membranes that enclose a single lumenal space (1). Several studies have ...