It is now recognized that microorganisms form the foundation of life on Earth. In marine ecosystems, microbes are the main primary producers, fixing carbon dioxide into organic material, and the primary consumers of organic matter, respiring carbon dioxide to the surrounding seawater and ultimately the atmosphere. Over the last twenty years, marine microbial ecologists have employed molecular biology-based techniques to achieve an appreciation for the complexity of aquatic microbial communities. These assemblages are comprised of genetically distinct populations, each responsible for mediating critical pathways in the cycling of organic carbon, nutrients, and energy. Microbial community structure is therefore a critical determinant of the biogeochemical processes occurring within seawater ecosystems.