A systematic approach to the model order reduction of high fidelity coupled fluidstructure/flight dynamics models and the subsequent control design is described. It uses information on the eigenspectrum of the coupled-system Jacobian matrix and projects the system through a series expansion onto a small basis of eigenvectors representative of the full-model dynamics. A nonlinear reduced order model is derived and is exploited for a worst case gust and adaptive control design. The investigation focuses on a flight control design based on the model reference adaptive control scheme via the Lyapunov stability approach. The novelty of this paper is two-fold. Firstly, it uses a single nonlinear reduced model for parametric worst case gust search. Secondly, it is shown that it makes feasible an implementation of a complex control methodology for a large nonlinear system. The adaptive controller is able to alleviate gust loads for a three degrees-of-freedom aerofoil and for an unmanned aerial vehicle. An investigation for the adaptation parameters is performed and their effect on control input actuation and aeroelastic closed-loop response is discussed.= plunge stiffness,torsional and flap stiffness about elastic axis= plunge, torsional and flap third order terms of stiffness