Ecological research of microorganisms sensu latu (archaea, bacteria, protists, viruses) has come of age within the last few decades. This newfound importance is a consequence of a greater appreciation for the enormous diversity present among these unseen entities, and an increasing recognition of the pivotal roles that these species play in food-web processes and geochemical cycles in aquatic and terrestrial ecosystems. These advances are due in large part to the incorporation of modern genetic and immunological approaches into ecological and physiological studies of natural assemblages and pure cultures of microorganisms. Molecular approaches have revolutionized bacterial and archaeal biology, and are beginning to transform our understanding of protistan ecology (unicellular eukaryotic algae and protozoa). Recent efforts have greatly improved our comprehension of the evolutionary relationships among protistan taxa; documented the existence of lineages of previously undetected protists; and catalyzed studies characterizing their diversity, nutritional modes, and trophic interactions. These extraordinary findings are only beginning to unfold as genetic databases for protists expand and as ecologists learn to interpret and exploit this wealth of genetic information.