A major challenge in marine microbial ecology is understanding the origins and functional role of taxonomic and genomic diversity among microorganisms in the ocean. Within a species, strains can demonstrate markedly different genomic properties, physiologies, and ecologies. Since its discovery in 1950, numerous studies have identified phylogenetically and ecologically distinct lineages or ecotypes. Even within ecotypes, subpopulations of Synechococcus have been identified, separated by genomic areas of flexibility hypothesized to confer ecological distinction and protection from viral lysis and grazing. Given their global abundance, and ecological importance, Synechococcus provides an excellent model system to explore how the genomic differences influences their physiology and ecological distribution..