This paper deals with modelling and identification of a shipboard stabilized satellite antenna system using the optimal neural network structure. It is difficult for shipboard satellite antenna system to control and identification because of their approximating ability of nonlinear function So it is important to design the neural network with optimal structure for minimum error and fast response time. In this paper, a neural network structure using genetic algorithm is optimized And genetic algorithm is also used for identifying a shipboard satellite antenna system It is noticed that the optimal neural network structure actually describes the real movement of ship well. Through practical test, the optimal neural network structure is shown to be effective for modelling the shipboard satellite antenna system.