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Industrial robots are required to have light weight structures in order to increase the payload to weight ratio and to lower the energy consumption Because of the flexibility, udesirable vibration occurs during motion. In this paper, a flexible two-link three-degree of freedom experimental manipulator is treated. The links flexibility is represented using finite element approximation. For this model, the equations of motion derived using Lagrangian Dynamics. Based on the model reference adaptive control approach, a general nonlinear controller is derived for manipulators with flexible links. Simulation results for the controller show its superiority over a linear regulator. Finally, by changing the end point mass, it is shown that under the adaptive controller, the robot retains good performance.