Hybrid systems consist of continuous and discrete dynamics. These systems can be described with a set of modes, where in each mode the system is governed by a continuous dynamics, and different modes correspond to different continuous models. For hybrid systems, model-based fault detection and isolation (FDI) is a challenging task, since system's prevailing dynamical model and the system's current mode (discrete state) are mutual dependent and intertwined. This paper introduces a new energy based approach for mode tracking of physical systems with hybrid dynamics. A Hybrid Bond Graph systematic analysis is utilized to characterize each system's mode with compact energy relations. To track system's modes, we monitor these energy relations in real time. The result is an energy based mode tracker that is more efficient in terms of computational resources than existing techniques.