The motion control of autonomous underwater vehicles (AUVs) is affected by waves near the ocean surface or in shallow-water areas. Therefore, to counteract the influence of waves, we need to remove them by designing a filter. The wave peak frequency is important in wave filter design. This paper focuses on the identification of the wave peak frequency using the least-squares parameter estimation algorithm. The input–output expression of the wave disturbance model is derived by eliminating the intermediate variable. Based on the obtained identification model, an auxiliary model-based recursive extended least-squares identification algorithm is developed to estimate the model parameters. The effectiveness of the proposed method is verified with simulated tests of the heading control system of an AUV. The simulation results demonstrate that the proposed method is effective for the identification of the wave peak frequency, and an observer with a wave peak frequency tracker can significantly reduce invalid steering.