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Mean Value Engine Models, commonly used for model based fault diagnosis of SI engines, fail to capture the within-cycle dynamics of engines, often resulting in reduced fault sensitivity. This paper presents a new Hybrid Automata based modeling approach for characterizing the within-cycle dynamics of the thermo-fluidic processes in a Spark Ignition Gasoline Engine, targeted for use in model based fault diagnosis. Further, using a hybrid version of the Extended Kalman Filter (EKF), the states from the nonlinear hybrid automata based dynamic model are estimated and their results validated w.r.t standard industrial simulation software, AMESim. It is observed that due to the switching of within cycle engine dynamics, causing mode change, there is a corresponding change in model's structure which in turn can cause change in system's observability.