Multi-Agent Systems (MASs) have received much attention in recent years because of their advantages on modeling complex distributed systems, such Digital Ecosystems (DESs). Many existing modeling languages that support the design of such systems are based on ontologies to assist the representation of agents knowledge. However, in the context of DESs, there is still a need for more general conceptual models to represent the specific characteristics of DESs in terms of win-win interaction, engagement, equilibrium, and self-organization. Then, concepts such behavior, roles, rules, and environment are needed. This paper describes an ontology-based approach by proposing MAS2DES-Onto, as the conceptual model, which considers the essential static and dynamic aspects of MASs by a clear representation of their concepts and relationships to support the design and development of DESs. To validate and conduct experimental tests, we integrate MAS2DES-Onto into a framework to automatically generate MAS-based DESs. Results show the efficiency and effectiveness of our approach.