Standardized ecological classification units form the foundation for effective data collection, assessment, and reporting on ecosystems. Attempts at regional land cover mapping often falter on this point or struggle along inefficiently. Over the past decade, NatureServe has worked with the Gap Analysis Program and others to map existing vegetation using the US National Vegetation Classification (US-NVC). US-NVC is a system of hierarchical structure and rules that are designed to provide a national classification of existing vegetation. Experience has demonstrated the need to develop map units at conceptual scales intermediate between the narrowly specific alliance (floristic) and the broadly generalized formation (physiognomic) levels of the US-NVC. NatureServe defined over 630 “mesoscale” vegetation-based units that are described across the lower 48 United States. These mesoscale classification units, which we term “terrestrial ecological systems,” are described using multiple plant communities that tend to co-occur based on recurrent similarities in environmental setting and ecological dynamics. By integrating environmental setting and ecological processes with vegetation into the concept of each unit, this classification system lends itself to biophysical modeling and robust characterization of wildlife habitat. These units apply well to land cover mapping and may be augmented with modifiers for specific variants in composition and structure resulting in robust, standardized maps. Regional-scale mapping of “near-natural” land cover was completed by the Southwest Regional Gap Analysis Project using 109 ecological system units, currently the most detailed regional land cover map of its kind. Terrestrial ecological system units provide a direct, systematic link to the US National Vegetation Classification and may also provide a useful framework for integration with ecological site concepts and descriptions.