The objectives of this paper are (a) to motivate the adoption of semantic graphical models of threat relations and countermeasures in the design and operation of cyber‐physical systems (CPS), and (b) to raise awareness of the various benefits which systems security engineers (SSEs) stand to gain by adopting such practices. Specifically, we propose that a Semantic Threat Analysis (STA) can endow SSEs with a comprehensive, extensible, machine‐readable, and logically inferable model of system features. An STA shaped to the specific architecture and security requirements of a CPS environment can support the identification and visualization of system interdependencies and process flows among network, computing, mechanical, security, and access control components. The proposed STA process presupposes a team‐oriented systems engineering approach employing a combination of subject matter experts (SMEs) and ontologists who can bring their respective expertise together to bear on the task.