A major transition became necessary for the maritime industry to meet the IMO’s targets for mitigating the carbon footprint of the sector by at least 50% by 2050. One of the promising methods to lower the emissions is the ship's hybridization. An enormous increase in pilot and demonstration projects for that purpose is being observed. This research was contacted through the involvement of TU Delft in such a project called the Implementation of Ship Hybridisation. The design and optimization of hybrid propulsion systems is a complex and challenging task due to the different power sources involved and the dependence on the energy management and control. The physical system and the control algorithm should be designed in an integrated manner to obtain an optimal system design. This study applies a multi-objective double-layer optimization methodology to optimize the sizing and energy management of a hybrid ship propulsion system to be installed on a Crew transfer vessel. A proposed hybrid topology which combines diesel engines, batteries and fuel cells is considered. The proposed approach incorporates the development of fuels and electricity prices as well as the investment costs of the system’s components as an uncertainty element. The introduction of emission reduction measures such as carbon tax was also considered in the study. Future trajectories for the relevant uncertainties were developed and incorporated in the optimization methodology to provide decision-makers with a more realistic picture of the solution space. The analysis of the optimization results was based on the Total cost of ownership (TCO) and the emission reduction potential of the optimal designs produced by the optimization methodology. The results show that instead of choosing a hybrid propulsion system for the vessel under study, an all-electric propulsion system which is based entirely on batteries and fuel cells is the most economical and environmentally friendly option. Incorporating diesel engines has a negative impact on the operational expenditures of the system in the long term. A fully electric propulsion system would require a larger initial investment from the ship owner, but it would pay off over the course of the ship’s remaining useful life. This research can be used as a reference to base the decision of the stakeholders on choosing a new propulsive system for their vessel. The parameters of the optimization methodology can be easily changed to explore more options and expand the design solution space if this thesis’ results don’t satisfy the shipowner. In addition, it is suggested that a professional user interface designer be involved in the development of a real life decision support tool, incorporating the multi-objective optimization methodology.