Over the last several years, the IUCN Red List approach for assessing the risk of extinction faced by species has been adapted into a Red List of Ecosystems methodology. This endeavor faces several important challenges, including how to define the types of ecosystems to which the Red List criteria are applied, and how to manage information on the geographic distribution of ecosystems in an open, transparent, and standardized manner linking mapping, typology, and field studies. We propose a fundamentally novel approach that differs from currently available ecosystem typologies in three important aspects by (1) offering a new way of conceptualizing types of ecosystems, (2) providing an explicit method for communicating the conceptualized ecosystems and how they are circumscribed, and (3) developing technical tools for managing the resulting conceptual model. Firstly, ecosystem types are defined by studying biogeoclimatic gradients using an approach that is both modular (in which combinations of ecological factors are studied at a given scale) and hierarchical (involving relative spatial and temporal scales in which local/site gradients are dependent on bioclimatic/regional gradients). This avoids the problem of classes that are not mutually exclusive and enables the classification of all types of ecosystems, including for example marshes on rocky outcrops in superhumid tropical montane areas. Secondly, the names of ecosystem species are linked to a nomenclatural type defined by a ‘type site’ or ‘biotype’, adopting a principle that makes clear a given author's notion of an ecosystem type even if the accompanying name and description are partial or imperfect, or when the ecosystem type is delimited too broadly according to the interpretation of another author. Ecosystem names are structured as a descriptive diagnosis based on a standardized set of characters and character states. This typological approach for facilitating the naming and comparison of ecosystem circumscriptions is thus truly taxonomic in nature. Thirdly, in order to facilitate the use and application of the conceptual approach presented here, we translate it into a practical tool by developing a smartphone-based system to collect data for observing and describing virtual ecosystem specimens in the field, along with the "Bio" database, which manages ecosystem data and also enables tracking synonymies using an open system that entails assigning determinavits to biotypes.