Marine microbial communities were among the first microbial communities to be studied using cultivation-independent genomic approaches. Ocean-going genomic studies are now providing a more comprehensive description of the organisms and processes that shape microbial community structure, function and dynamics in the sea. Through the lens of microbial community genomics, a more comprehensive view of uncultivated microbial species, gene and biochemical pathway distributions, and naturally occurring genomic variability is being brought into sharper focus. Besides providing new perspectives on oceanic microbial communities, these new studies are now poised to reveal the fundamental principles that drive microbial ecological and evolutionary processes.