In this paper, an advanced power management and control strategy is proposed to manage the operation of a short-route all electric battery powered ferry. The objective of this strategy is to maintain reliable power supply for both propulsion and ferry service loads under all operations and achieve suitable exploitation of the batteries-based energy storage systems (BESSs). For this aim, and in order to achieve these objectives a hierarchical control strategy. This strategy includes an inner voltage-current control level to maintain the desired DC voltage at the onboard DC bus and a V/P droop-based power sharing control level to accurately share the power between BESSs. Additionally, an external power management level is implemented in order to define the power participation amount of each BESSs according to the ferry load power demand and to their state of charge (SOC). This power management strategy handles also the SOC balancing of the onboard BESSs using optimized participation factors. The optimized SOCs balancing aims at improving the performance and life cycles of the BESSs and avoiding excessive BESS discharge and disconnection. The validity of the proposed control and management strategy is verified using Hardware-in-the-Loop Simulation.