In this paper, we present an alternative approach to the automated aircraft identification system. This system differs from the one proposed in the earlier literature in two ways. First, it uses a general model of the aeronautical air-ground channel which takes into account multipath propagation and Doppler shift. Second, it uses Orthogonal Frequency Division Multiplexing (OFDM) rather than single carrier modulation. The resulting system is then implemented to evaluate the performance of an automatic aircraft identification for the future aeronautical communication system. This automatic identification is achieved by using Spread Spectrum watermarking which allows transmitting embedded digital identification data, such as call sign or tail number, within the speech signal sent by the pilot. We further analyze the impact of different parameters derived from the channel model through simulation results. The system performances are evaluated through transmission reliability and watermark extraction. The experiment results show the impact of channel modeling on the performances of the proposed system.