Roll motion affects the performance of seagoing surface vessels by limiting the effectiveness of the crew and also the operation of on-board equipment. Robust stabilization of roll motions is studied in this paper. The control system consists of a Fractional-Order PID (FOPID) controller based on a supervisory controller. The linear FOPID controller is adapted to carry out the feedback control system and the supervisory controller is developed guaranteeing the system stability. The supervisory controller is designed by means of Lyapunov direct method and stability of the closed-loop system in the presence of uncertainties and disturbances is proved via rigorous analysis. Then, a FOPID controller is employed to attain desired output. In order to determine appropriate values of control parameters Chaos embedded PSO (CPSO) algorithm is used. Numerical simulations have been carried out to verify the effectiveness of the controller. The effect of sinusoidal perturbations is also investigated. It is shown that the control system can stabilize the roll motion magnificently in the presence of uncertainties and disturbances.