In the Airborne Laser there are two wavefronts of interest, namely, the inbound wavefront from the beacon and the outbound wavefront of the high-energy laser. The beacon wavefront emanates from the tip of the missile, whereas the high-energy laser wavefront is directed towards the ami point on the missile. Hence, these two wavefronts propagate through different regions of the atmosphere at different time instants, which is the cause of anisoplanatism. In order to account for the anisoplanatic effect, the spatial- temporal correlation between the Zernike polynomials' phase distortion expansion coefficients representing these wavefronts must be determined. Using this correlation information, an underlying linear, stochastic, dynamical system, which represents the atmosphere, is identified. This linear system is the plant. The wavefront sensor and deformable mirror dynamics are also modeled.