The purpose of this dissertation is to develop a methodology for designing active control laws in a computational aeroelasticity environment. The methodology involves employing a systems identification technique to develop an explicit state-space model for control law design from the output of a computational aeroelasticity code. The particular computational aeroelasticity code employed in this dissertation solves the transonic small disturbance equation using a time-accurate, finite-difference scheme. Linear structural dynamics equations are integrated simultaneously with the computational fluid dynamics equations to determine the time responses of the structural outputs. These structural outputs are employed as the input to a modern systems identification technique that determines the Markov parameters of an "equivalent linear system". The eigensystem realization algorithm is then employed to develop an explicit state-space model of the equivalent linear system. Although there are many control law design techniques available, the standard Linear Quadratic Guassian technique is employed in this dissertation. The computational aeroelasticity code is modified to accept control laws and perform closed-loop simulations. Flutter control of a rectangular wing model is chosen to demonstrate the methodology. Various cases are used to illustrate the usefulness of the methodology as the nonlinearity of the computational fluid dynamics system is increased through increased angle-of-attack changes.