The thesis is presented that classical taxonomy is of limited value to ecosystem science, and that the further development of the ecosystem theory may actually be hindered by a reliance on the biological (phylogenetic) species as the basic functional unit of ecosystems. This situation probably would improve if ecologists agreed on a system of functional classification in which ecological taxa would be distinguished solely on the basis of what they do in the context of an ecosystem, and not on their evolutionary relationships. A functional classification system is proposed in which functional taxa for specific ecosystems (ecological sectors) are defined as broad trophic groups of organisms in common vertical habitat zones, and with common inputs and outputs (ecosystem commodities and services), This system is envisioned as potentially useful in the development of comparative ecosystem theory, for constructing simulation models, for ongoing research in economic vs. ecological values, and for cataloging new functional information as it becomes available. The proposed system is tentatively applied to the salt marsh estuarine ecosystem in the southeastern USA and to the swampforest ecosystem in Louisiana. In the former, 25 sectors are identified, in the latter, 20.
