During the 1980s, many new molecular biology techniques were developed, providing new capabilities for studying the genetics and activities of organisms. Biologists and ecologists saw the promise that these techniques held for studying different aspects of organisms, both in culture and in the natural environment. In less than a decade, these techniques were adopted by a large number of researchers studying many types of organisms in diverse environments. Much of the molecular-level information acquired has been used to address questions of evolution, biogeography, population structure and biodiversity. At this juncture, molecular ecologists are poised to contribute to the study of the fundamental characteristics underlying aquatic community structure. The goal of this overview is to assess where we have been, where we are now and what the future holds for revealing the basis of community structure and function with molecular-level information.