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The application of new molecular and genomic techniques to the ocean is driving a scientific revolution in marine microbiology. Discoveries range from previously unknown groups of organisms and novel metabolic pathways to a deeper appreciation of the fundamental genetic and functional diversity of oceanic microbes. The “oceanic genotype” represents only the potential biological capacity and sets an upper constraint on possible pathways and ecosystem rates. The realized structure and functioning of marine ecosystems, the “oceanic phenotype”, reflects the complex interactions of individuals and populations with their physical and chemical environment and with each other. A comprehensive exploitation of the wealth of new genomic data therefore requires a close synergy with interdisciplinary ocean research. Incorporating the information from environmental genomics, targeted process studies, and ocean observing systems into numerical models will improve predictions of the ocean's response to environmental perturbations. Integrating information from genes, populations, and ecosystems is the next great challenge for oceanography.