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In this paper, tracking control of underactuated ship in the presence of input saturation is addressed. By dividing the tracking error dynamic system into a cascade of two subsystems, the torques in surge and yaw axes are designed separately using the backstepping technique. More specifically, we design the yaw axis torque in such a way that its corresponding subsystem is finite time stable, which makes it to be de-coupled from the second subsystem after a finite time. This enables us to design the torque in the surge axis independently. It is shown that the closed-loop system is stable and the mean-square tracking errors can be made arbitrarily small by choosing design parameters. Simulation results also verify the effectiveness of the proposed scheme.