Modelling is an essential tool for the study and analysis of security properties in all kinds of digitally connected systems. Certainly, it can help current organizations to secure their critical assets and find practical solutions to cover potential new threats. This is, in fact, the main motivation behind the special issue presented here. It reports recent research works related to modelling security threats, agent misbehaviours and protection strategies for critical environments. Most of them assume environments such as cyber-physical systems or, in other words, classical control systems upgraded with novel computing, communication and interconnection capabilities via SCADA (Supervisory Control and Data Acquisition) technologies and industrial control protocols