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In this paper, robust adaptive control with dynamic control allocation is proposed for the positioning of marine vessels equipped with a thruster assisted mooring system, in the presence of parametric uncertainties, unknown disturbances and input nonlinearities. Using neural network approximation and variable structure based techniques in combination with backstepping and Lyapunov synthesis, the positioning control is developed to handle the uncertainties, input saturation and dead-zone characteristics of the mooring lines and thrusters. Full state feedback with all states measurable and output feedback using high gain observer to estimate unmeasurable states are considered. Dynamic control allocation is presented for actuation of the position mooring system. Under the proposed robust adaptive control, semi-global uniform boundedness of the closed-loop signals are guaranteed. Numerical simulations are carried out to show the effectiveness of the proposed control.