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The operation of high energy loads on the Navy's future electric ships will cause disturbances to the main bus voltage and impact the operation of the rest of the power system. This paper describes an online design and laboratory hardware implementation of an optimal excitation controller using an artificial immune system (AIS)-based algorithm. The AIS algorithm, a clonal selection algorithm (CSA), is used to minimize the effects of pulsed loads by improved excitation control and reduce the requirement on energy storage device capacity. The CSA is implemented on the MSK2812 DSP hardware platform. A comparison of CSA and the particle swarm optimization algorithm is presented. Both simulation and hardware measurement results show that the CSA-optimized excitation controller provides effective control of a generator's terminal voltage during pulsed loads, restoring and stabilizing it quickly.