-A novel robust adaptive PID control scheme is proposed with known upper bound of the external disturbances, to solve the dynamic coupling and strong nonlinearity problems in flexible joint robot manipulator control. Invoking the proposed controller, the bounded external disturbances can be compensated and the global asymptotical stability with respect to the manipulator positions and velocities is able to be guaranteed. The designed control law can enlarge the tolerable external disturbances, enhance the accuracy of trajectory tracking error, and improve the dynamic performance of the manipulator systems. The stability and convergence properties of the closed-loop system are analytically proved using Lyapunov stability theory and Barbalat's lemma. Simulation for the proposed control system is performed for a two-degree of freedom flexible joint robot, each joint modeled by two-equations of second order to illustrate its viability, and advantages.