In recent years, developments in the field of aerospace materials and structures has been bringing major breakthroughs in the construction of air vehicles to be more lightweight yet with higher strength. However, the aircraft body can deform more appreciably due to the occurrence of flow separation and flutter. Therefore, active control is necessary in order to maintain structural integrity. One of the proposed control methods uses visual tracking for structural state estimation which reduces complexity in terms of hardware and data processing requirements compared to the conventional method of inserting a large number of inertial measurement units and gyroscopes in wing sections. The visual tracking routine is then integrated into a new structural state estimation routine that is robust against optical occlusions, and that can accurately reconstruct the states of the complete aeroelastic system. A new idea is to use a state estimator based on a reduced order mathematical model of the aeroelastic wing. This new state estimator is validated in simulation in different gust regimes. The results show that the state estimation convergences to the true values despite the process and measurement noise present in all simulated flight conditions. However, the pole position of the reconstructed state space fails to mimic the stable characteristics of the true model. Further analysis is recommended to constrain the parameter estimation in order to ensure that the stability of the true model can be retained, yielding an accurate solution for the aeroelastic controller feedback.