In this paper, control design of an elastically shaped aircraft with highly flexible wings is discussed. The aircraft has the capability to actively change the wing twist and bending in flight so as to achieve a local angle of attack distribution that is optimal for the specific flight condition. The aircraft has 23 control surfaces and is longitudinally unstable in the open loop. Two design approaches are explored. In the first approach, a multi-objective performance index that includes an explicit drag minimization term is considered, and an optimal controller design is performed using this performance index. In the second approach, a decentralized controller that uses the elevator to control only the rigid body modes, and the wing flap and slat control surfaces to control the flexible modes, is developed. Simulation results demonstrate the validity of these controllers in stabilizing this elastic aircraft.