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The model reference adaptive control of a two axis direct drive manipulator arm is presented. The two axes exhibit a significant dynamic interaction. The model reference adaptive controller is utilized in the velocity loop to adaptively decouple the dynamic interaction and to linearize the dynamics. The outer loop controller for positioning and tracking is designed based on the linear decoupled dynamics. The adaptive velocity loop controller as well as position loop controller are implemented digitally. The use of a series-parallel, as well as a parallel reference model is suggested in the adaptive velocity loop controller. The stability problems arising from the straightforward digital implementation of the continuous time algorithm are analyzed and a modification in the digital algorithm is introduced which guarantees the asymptotic stability of the system. Simulation and experimental results show a consistently superior performance of the manipulator under adaptive control.