In the field of naval operations, the traffic control and the location of unregulated vehicles are of vital importance to the traffic of ports, governments and naval military forces, among others this helps to control the security and sovereignty of certain areas. Processing the underwater acoustic signals using methods such as MPM for its complex natural resonance extraction can be an effective but challenging way for identification of these ships. In this paper, we show that in the presence of a stable medium, it is possible to determine the principal frequency components related ships in a classification process. The analysis was developed using 30 signals of a cargo vessel ship, 66 of a frigate and 69 of a subchaser. Results show that the total averages of the poles of the ships are in specific regions of the plane, however, the analysis of the imaginary quantities of the complex natural resonances may bring a better insight for the identification process.