This paper proposes an autonomous system identification methodology for fixed wing autonomous aerial vehicles (AAVs) and implementation with a robust control technique. This system identification methodology does not require the user to provide any knowledge of the aerodynamic derivatives of the AAV. Hence, this control methodology is applicable to a wide range of fixed-wing AAVs. Since the system identification process generates errors due to the measurement noise and external disturbances, a robust control methodology, slidingmode control (SMC), is proposed to control the AAV based on the system identification results. To characterize the capability of the control methodology, experiments have been conducted on commercially available fixed-wing aircraft platforms using low-cost sensing equipment. Experimental results demonstrate that the autonomous system identification-based SMC enables the AAV to follow the desired trajectory without prior knowledge of the aerial vehicle or manual tuning of control system parameters.