Effective management of our natural resources requires an understanding of ecosystem structure and function; effectively, an ecosystem-based approach to management. Parasites occur, albeit cryptically, in almost all ecosystems, yet they are usually neglected in studies on populations and communties of organisms. Parasites can have pronounced or subtle effects on hosts affecting host behavior, growth, fecundity, and mortality. Furthermore, parasites may regulate host population dynamics and influence community structure. Many parasites have complex life cycles and depend for transmission on the presence of a variety of invertebrate and vertebrate intermediate hosts. Often transmission involves predator-prey interactions. Thus, parasites reflect the host's position in the food web and are indicative of changes in ecosystem structure and function. Parasites can provide information on population structure, evolutionary hypotheses, environmental stressors, trophic interactions, biodiversity, and climatic conditions. I use examples from diverse freshwater and marine systems to demonstrate that parasites should be incorporated into research and monitoring programs to maximize information gathered in ecosystem-based studies and resource management.