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In this paper, a novel robust adaptive control algorithm is proposed for a class of ship course autopilot with parameter uncertainty and input saturation. With the help of Lyapunov stability theory and adaptive backstepping technique, one controller is constructed by considering parameter uncertainty and actuator saturation constraints, and the stability analysis subject to the effect of input saturation constrains is conducted by employing an auxiliary design system. It is also proved that the proposed algorithm could guarantee the closed-loop system to be uniformly ultimately bounded and the output converges to a small neighborhood of zero. Simulation results are given to illustrate the effectiveness and the performance of the proposed scheme.