In real system application, the propeller shaft rate (PSR) estimation algorithm for the feature extraction of the sonar target operates with the following problems: it requires both accurate and efficient the fundamental finding method because it is essential and difficult to distinguish harmonic family composed of the fundamental and its harmonics from the multiple spectral lines in the frequency spectrum-based sonar target classification, and further, it requires an easy design procedure in terms of its structures and parameters. To solve these problems, an evolutionary PSR estimation algorithm using an expert knowledge and the evolution strategy, is proposed. To verify the performance of the proposed algorithm, a sonar target PSR estimation is performed. Simulation results show that the proposed algorithm effectively solves the problems in the realtime system application.