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In this paper the control of a flexible joint manipulator is designed using an adaptive output-feedback controller based on the backstepping design. The parameters of system are assumed to be unknown and only the motor position and link position measurements are used for the synthesis of the controller. A canonical state representation of the system is derived and filters are designed to obtain estimates of the derivatives of motor angle and link angle. Then an adaptive control law for the trajectory control of link displacement angle is derived. Compared to the same adaptive controller which only measures the link displacement angle, the order of the proposed controller is halved (order of 2) and the complexity of the control law can be reduced dramatically. Also, the proposed controller does not require the bounds on uncertain parameters for the control law derivation as compared to other output adaptive control laws.