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The problem of designing and developing a hybrid fault detection and isolation (FDI) scheme for a non-linear system that is subject to large environmental disturbances is investigated. In the proposed FDI scheme, a hybrid architecture is introduced, which is composed of a bank of residual generators and a discrete-event system (DES) fault diagnoser. A novel set of residuals is generated so that a DES fault diagnoser will robustly detect and isolate actuator faults in the system by incorporating an appropriate combination of residuals and their sequential features. Necessary and sufficient conditions for the existence of a set of residuals that are used by the DES fault diagnoser are derived based on the non-linear geometric FDI approach. The proposed hybrid FDI scheme is then applied to actuator fault detection and isolation of an almost-lighter-than-air-vehicle. Simulation results presented demonstrate and validate the performance capabilities of the proposed hybrid FDI scheme.