As a result of previous efforts [Pachter, Barba, 2007] a tight control loop was designed to meet performance specifications while minimizing the feedback control system’s gains of a spacecraft mounted flexible antenna. Emphasis is now shifted to on orbit system identification of the antenna dynamics in order to increase nominal plant knowledge, estimate plant uncertainty bounds, as well as determine the disturbance band. Non-parametric system identification is undertaken. Knowledge of the plant dynamics along with the corresponding uncertainty bounds will provide for the design of a control system which meets the specifications (tracking and disturbance rejection) while at the same time employing the lowest possible gain. This in turn is conducive to sensor noise disturbance rejection, avoidance of actuator saturation, and excitation of high frequency modes