In this paper, we propose an observer-based adaptive output feedback flight tracking system for the miniature aerial vehicle (MAV) in the presence of bounded uncertainty. The proposed design has two parts. First, a state feedback based nonlinear adaptive control algorithm is designed by assuming that all the states are available for feedback. The convergence analysis with the state feedback based design is derived by using the Lyapunov method. Second, we replace the unknown velocity states by a linear observer to develop adaptive output feedback flight tracking system for the MAV. The convergence analysis with the observer-based output feedback design is shown by using a singularly perturbed method. The analysis shows that the performance achieved under state feedback can be recovered by using an output feedback based design. Evaluation results are given to demonstrate the effectiveness of the proposed design for real-time applications.