The competitive market poses high requirements to automation systems. Fulfilling considerable requirements concerning flexibility, availability and efficiency, they have become complex mechatronic systems, featuring both discrete and continuous behavior. For reducing efforts concerning time and costs during the life cycle of production plants, simulation methods are widely applied in the development process. In the operation phase, the identification and analysis of failures is fundamental. Bearing the challenges of hybrid automation systems, a methodology is proposed, realizing monitoring and diagnostics based on a simulation approach. Therein, a simulation represents the behavior of the system and the control system.