This paper presents a comparative study to determine the optimal combination of hybrid energy storage system used on Shipboard Power System (SPS). The hybrid energy storage comprises two or more types of energy storage elements (Batteries, Ultra-Capacitors and Flywheels). In this research work, the optimal combination of these three types is determined to minimize the voltage and frequency fluctuations caused by the connection of pulsed loads on the AC or DC sides of the system. A model for hybrid AC/DC SPS with zonal distribution architecture was built in DIgSILENT PowerFactory software. Several case studies are carried out and their results are compared and analyzed.