Cyanobacteria (oxygenic photosynthetic bacteria) are complicated prokaryotes, incorporating a cell wall similar to other Gram-negative bacteria, internal thylakoid membranes, in which photosynthesis and energy generation occur, and carboxysomes, the site of carbon fixation. Cyanobacteria are also potential platforms for synthetic biology applications, given their ability to convert solar energy efficiently into biomass. However, our understanding of these organisms, especially how proteins are targeted to different compartments, is limited. Using subcellular fractionation and quantitative proteomics we have developed the most extensive subcellular map of the proteome of a cyanobacterial cell, identifying ~67% of Synechocystis sp. PCC 6803 proteins and mapping 1,711 proteins to six specific subcellular regions. Combined with genetic and bioinformatics tools we have developed, this has allowed us to generate optimised strains for industrial applications. For example, we have successfully targeted proteorhodopsin, a green light absorbing, proton pumping protein, to thylakoid membranes. This resulted in a recombinant strain with improved growth and 18% higher biomass accumulation. Another strain, in which five electron sinks were deleted, demonstrates power output of 0.53 W m-2 in biophotovoltaic devices, which uses photosynthetic organisms to convert sunlight into electricity. In this talk I will discuss these tools and developments, and how they can be applied to further develop strains for production of biofuels, industrial chemicals and electricity.