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In this paper a novel optimal approach of control strategy is introduced by applying fractional calculus in the structure of sliding mode control for a range of dynamics system liable to ambiguity. So, a fractional sliding mode control was designed for dynamics of the two-link rigid-flexible manipulator. Furthermore, a multi-objective genetic algorithm was proposed in order to find the ideal variable structure of the sliding mode control. Optimal variables were achieved by the optimization of the conventional sliding mode control. Then the performance of both the conventional and the fractional sliding mode control were compared with respect to optimal variables. Results indicated that by applying the optimized fractional sliding mode control, the system's error was significantly reduced consequently tracking the desired value was done with a higher degree of accuracy and a smoother control action was achieved.