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First, an auxiliary derivative output of dynamic positioning ships is constructed in order to satisfy the so-called observer matching condition, and a high-gain observer is designed to exactly estimate the auxiliary derivative outputs. Then, a fault-tolerant controller is developed for dynamic positioning ships based on the iterative learning observer. By means of Lyapunov-Krasovskii stability theory, it is proved that the proposed fault-tolerant controller is able to estimate the total fault effects and states of ships accurately via the iterative learning observer and also to stabilize the closed-loop system. In addition, the parameter design of the proposed fault-tolerant control system can be conveniently solved in terms of linear matrix inequalities. 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