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All-electric ships, and especially the hybrid ones with diesel generators and batteries, have attracted the attention of maritime industry in the last years due to their less emission and higher efficiency. The variant emission policies in different sailing areas and the impact of physical and environmental phenomena on ships energy consumption are two interesting and serious concepts in the maritime issues. In this paper, an efficient energy management strategy is proposed for a hybrid vessel that can effectively consider the emission policies and apply the impacts of ship resistant, wind direction and sea state on the ships propulsion. In addition, the possibility and impact of charging and discharging the carried electrical vehicles’ batteries by the ship is investigated. All mentioned matters are mathematically formulated and a general model of the system is extracted. The resulted model and real data are utilized for the proposed energy management strategy. A genetic algorithm is used in MATLAB software to obtain the optimal solution for a specific trip of the ship. Simulation results confirm the effectiveness of the proposed energy management method in economical and reliable operation of the ship considering the different emission control policies and weather condition impacts.