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A new adaptive control strategy based on artificial immune system (AIS) for a DSTATCOM in an electric ship power system is presented in this paper. DSTATCOM is a shunt compensation device, which can be used to improve the power quality during the pulse power requirements in a naval shipboard system. The role of DSTATCOM controller is very important to meet this objective. In this paper, the DSTATCOM controller parameters are first tuned by particle swarm optimization (PSO) technique, so that it can provide innate immunity to common system disturbances. Then, these optimum parameters are modified online by an artificial immune system (AIS), which provides adaptive immunity to unusual system disturbances. To evaluate the performance of the proposed control strategy, a simplified model of the ship system consisting of a 45 MVA main generator, a 5 MVA auxiliary generator and a 36 MW propulsion motor is simulated in a real-time environment. The effectiveness of the PSO and AIS based adaptive controller is demonstrated on a real time digital simulator based test system for pulsed loads of different magnitudes and durations.