Flight vehicles may contain some of structural nonlinearities such as freeplay, bilinear and hysterisis. These nonlinearities affect the aeroelastic characteristics significantly and may cause limit cycle oscillation(LCO) or chaotic motion below or above the linear flutter boundary. Although the LCO and the chaotic motion do not cause the abrupt failure of a structure, these motions can cause a damage by fatigue or a degradation of the control performance. Thus, it is important to understand the nonlinear aeroelastic characteristics of flight vehicles in the design stage. In this study, nonlinear aeroelastic characteristics of an aircraft wing and a missile control fin with structural nonlinearity are investigated and the flutter suppression is performed. First, the efficient and accurate methods for linear and nonlinear aeroelastic analyses are developed and verified. Secondly, the structural nonlinearities are identified from dynamic test data using the system identification. The estimated nonlinearities are linearized using a describing function and used in the nonlinear aeroelastic analysis. Thirdly, the linear and nonlinear aeroelastic analyses of a fighter-type wing with control surface and a deployable missile control fin are performed and the aeroelastic characteristics are investigated. Finally, the flutter suppression of wing/store model with a freeplay is performed using a sliding mode control. Nonlinear aeroelastic results show that the aeroelastic characteristics of flight vehicles with structural nonlinearities are significantly dependent on those modes and frequencies. Flutter suppression results show that a sliding mode control can give a good control performance for the nonlinear aeroelastic system.