During the 1980s, many new molecular biology techniques were developed, pro
viding new capabilities for studying the genetics and activities of organis
ms. Biologists and ecologists saw the promise that these techniques held fo
r studying different aspects of organisms, both in culture and in the natur
al environment. In less than a decade, these techniques were adopted by a l
arge number of researchers studying many types of organisms in diverse envi
ronments. Much of the molecular-level information acquired has been used to
address questions of evolution, biogeography, population structure and bio
diversity. At this juncture, molecular ecologists are poised to contribute
to the study of the fundamental characteristics underlying aquatic communit
y structure. The goal of this overview is to assess where we have been, whe
re we are now and what the future holds for revealing the basis of communit
y structure and function with molecular-level information.