The aim of this paper is to determine the mathematical relationship (model) between control deflections and structural deflections of the F/A-18 modified aircraft in the active aeroelastic wing technology program. Five sets of signals from flight flutter tests corresponding to the excited sources were measured by NASA Dryden Flight Research Center. These excitation inputs are: differential ailerons, collective ailerons, collective stabilisers, differential stabilisers, and rudders. The signals to be used by the model are of two types: control deflection time histories and corresponding structural deflections on the wing and trailing-edge flaps. We choose to use the subspace identification method based on reconstructing the observability matrix in order to identify the nonlinear multi-input, linear-in-the-states, multi-output system. We identify models (input/output characteristics) by applying this method for a number of sixteen flight conditions for which the Mach number varies from 0·85 to 1·30 and the altitudes vary from 5,000ft to 25,000ft. Very good results are obtained with a fit between the estimated and the measured signals and a correlation coefficient higher than 90%.