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This paper compares two nonlinear control strategies for a hybrid source system using an isolated three-port bidirectional full-bridge DC-DC converter. The system uses a fuel cell (FC) as a main energy source, a supercapacitor bank (SC) as an auxiliary source and a load. The first control strategy includes nonlinear and PI controller for which the dynamic response depends on the operating point. The second control strategy is based on the flatness controller which is independent from the operating point. The two control strategies allow taking into account practical constraints of the sources. Through experimental results, the proposed controllers are validated.