In an age of comparative microbial genomics, knowledge of the near-native architecture of microorganisms is essential for achieving an integrative understanding of physiology and function. We characterized and compared the three-dimensional architecture of the ecologically important cyanobacterium Prochlorococcus in a near-native state using cryo-electron tomography and found that closely related strains have diverged substantially in cellular organization and structure. By visualizing native, hydrated structures within cells, we discovered that the MED4 strain, which possesses one of the smallest genomes (1.66 Mbp) of any known photosynthetic organism, has evolved a comparatively streamlined cellular architecture. This strain possesses a smaller cell volume, an attenuated cell wall, and less extensive intracytoplasmic (photosynthetic) membrane system compared to the more deeply branched MIT9313 strain. Comparative genomic analyses indicate that differences have evolved in key structural genes, including those encoding enzymes involved in cell wall peptidoglycan biosynthesis. Although both strains possess carboxysomes that are polygonal and cluster in the central cytoplasm, the carboxysomes of MED4 are smaller. A streamlined cellular structure could be advantageous to microorganisms thriving in the low-nutrient conditions characteristic of large regions of the open ocean and thus have consequences for ecological niche differentiation. Through cryo-electron tomography we visualized, for the first time, the three-dimensional structure of the extensive network of photosynthetic lamellae within Prochlorococcus and the potential pathways for intracellular and intermembrane movement of molecules. Comparative information on the near-native structure of microorganisms is an important and necessary component of exploring microbial diversity and understanding its consequences for function and ecology.Environmental and culture-based comparative genomic analyses have established that closely related bacteria can exhibit considerable genetic diversity (2,38,39,48). Information on the comparative, near-native cellular structures of closely related microorganisms is an important component of understanding the functional consequences and significance of their genomic diversity. Although this has been studied intensively in heterotrophic bacteria, much less is known in this regard about the ecologically significant group of microbial phototrophs that play key roles in oxygen production, carbon fixation, and global biogeochemical cycles. Prochlorococcus is a globally important cyanobacterium that contributes nearly half of the net primary production in certain open ocean regions (3,7,14,18,35,50,52). Using cryo-electron tomography, we characterized and compared the three-dimensional (3D) structure of two Prochlorococcus strains in a near-native state. The two strains selected for this study represent the major Prochlorococcus ecotypes, eMIT9313 and eMED4 (18). MIT9313 belongs to a deeply branched clade and possesses a genome size...