This interdisciplinary project aims at elaborating an original framework to individuate ecosystems by combining conceptual, theoretical and modelling approaches. Ecosystems are not as bounded as typical biological individuals (i.e. organisms) but, rather, their boundaries appear fuzzy and porous. This is a problem for theorizing as such, but conservation and management should also rely on well-grounded criteria to delimit ecosystems and the functions of their components. We submit that ecosystems’ individuation goes hand in hand with their stability and resilience. The project explores how ecosystems, which show highly improbable regimes of order, maintain themselves in the biosphere by constraining the flow of matter and energy. Our working hypothesis is twofold: first, constraints are exerted by biodiversity items and abiotic factors, which can be understood as functional parts of the system; second, functional constraints realize a regime of mutual dependence, which provides a criterion to draw the boundaries of the overall ecosystem. The organization of constraints is therefore the theoretical principle that, at the same time, accounts for the stability of ecosystems, individuate them in space and time, and identify their functional components. The project intends to explore the conceptual and theoretical implications of this framework, and its capacity to guide the elaboration of specific mathematical and computational models of ecosystemic organization and eco-evolutionary dynamics. The inquiry about the individuation of ecosystems will be conducted by jointly considering different levels of biological organization. In particular, the project will analyze the analogies, dissimilarities and interactions between ecosystems and organisms: not only ecosystems are a different class of individuals when compared to organisms but, crucially, they are so because they are composed by organisms.