This article presents an innovative approach to address a rapidly evolving and polymorphic threat environment related to the emergence of the Internet of Things in the global Internet, with a focus on Cyber Physical Systems, Cloud architecture and SDN/NFV technologies. The article presents the view and methodological approach of ANASTACIA research project to address this evolution. ANASTACIA researches, develops and demonstrates a holistic solution enabling trust and security by-design for cyber physical systems (CPS) based on IoT and cloud architectures.