Model based development based on different domain specific tools and graphical notations gains increasing importance in system design of embedded electronic systems allowing fast concept-oriented prototyping from model to code. This paper describes an extension to our seamless model based development approach: An architecture for debugging models that are executed on target systems or in dedicated rapid-prototyping environments. We discuss the advantages of such an approach as opposed to simulation and describe our universal architecture. We focus on the definition of MOF-based runtime models and their synchronisation with the runtime target state. An example of debugging state-charts shows the feasibility of the approach.