In this thesis, spectral identification and design and implementation of the  controller for flexible joint robot (FJR) is presented and the capability of the controller to deal with actuator saturation is investigated in practice. The experimental procedures are introduced to regulate the frequency resolution of the spectral identification for both two links. The new procedure of design is introduced for the 2 link to avoid an instability caused by unmodeled phase behavior which cannot be encapsulated in multiplicative uncertainty. In order to avoid instability caused by unmodeled phase behavior, the robust controller design is divided into two stages:  controller design and checking closed loop sensitivity function. Simulation results reveal the capability of the controller to stabilize the closed loop system and to reduce the tracking error in the presence of the actuator limitation. Finally, the effectiveness of Robust Decentralized control has been checked for motion control of the links at the same time.