In this paper, we set up a mathematical framework for the modelling and control of complex cyber-physical ecosystems. In our setting, cyber-physical ecosystems (CPES) are cyber-physical systems of systems that are highly connected. CPES are understood as open and adaptive cyber-physical infrastructures. These networked systems combine cyber-physical systems with an interaction mechanism with other systems and the environment (ecosystem capability). The main focus will be on modelling cyber and physical interfaces that play an important role on the control of the emergent properties like safety and security.