Maritime transportation accounts for about 2.9% of global greenhouse gas (GHG) emissions, according to the fourth International Maritime Organization (IMO) GHG study. In the period from 2012 to 2018, shipping emissions have increased by almost 10%. Facing growing political and societal pressure, the IMO has established GHG emissions reduction targets consistent with the Paris Agreement temperature goals, aiming to reduce the total annual GHG emissions by at least 50% by 2050 compared to 2008 levels. In this context, alternative fuels and innovative technologies are needed to allow the maritime industry to comply with forthcoming regulations, as well as to fulfil decarbonisation targets within the European and the global markets.The shipping industry has already started to transition from traditional marine fuels, such as heavy fuel oil and marine diesel oil, to Liquified Natural Gas (LNG) in Internal Combustion Engines (ICEs). However, this can only be regarded as a bridging solution. In recent years, three major research lines can be identified: First, battery-electric propulsion, exploring the potential benefits of shaving peak thruster power and improving the energy efficiency and range of ships. Second, Solid Oxide Fuel Cells (SOFCs), which have a marked advantage of fuel flexibility and offer higher electrical efficiencies than ICEs and other fuel cell technologies, as well as higher-grade waste heat. Third, alternative marine fuels, such as synthetic hydrocarbons, biofuels, ammonia and hydrogen, as a way to significantly reduce or even phase out GHG emissions and other air pollutants.The present study bridges the aforementioned research lines by proposing a novel integrated marine energy system composed of an SOFC-battery hybrid genset that consumes LNG. The objective is to perform a techno-economic assessment of the hybrid genset for LNG and four identified potential alternative fuels (i.e. methanol, diesel, ammonia, and hydrogen). The best solutions will be identified and analysed, and a decision-making framework will be proposed. The comparison will identify the critical conditions for the genset processes being competitive to the state-of-the-art engine-based energy system.The analysis is divided into two main parts. The first part is dedicated to the SOFC module, which is composed of the SOFC stack and the balance of plant equipment. The BOP includes fuel storage, reformer, combustor, heat recovery system, pumps, and blowers. Previous work by the authors has developed the thermodynamic analysis of the genset systems that provide the starting point for the present analysis. The flow-sheet software Cycle Tempo was used in those analyses. The SOFC module has a nominal power production of 100 kWe, which is achieved by combining several stacks of 10 kWe, and produces hot water at 90 °C and saturated steam at 180 °C from waste heat recovery.In the second part, the SOFC-battery hybrid genset is achieved by combining several 100 kWe SOFC modules into power blocks and hybridizing them with batteries. The systems are designed to cover all the electricity and heat demands of the vessel, including propulsion and hotel load. A representative electrical demand of a large cruise ship is selected in the range of 30-60 MWe, of which about 80% is required for propulsion while the remaining is needed for the hotel.Among the main criteria for comparing the hybrid genset running on different fuels are the total annual cost, composed of the annual investment cost and annual operation cost, and the Levelized Costs of Energy, Electricity and Exergy. The latter is especially important because of the joint production of electricity and heat (saturated steam at 180 °C and hot water at 90 °C) that takes place in the genset. The investment cost was estimated using data collected from the literature or provided by manufacturers. The necessary replacement of SOFC stacks is taken into account, given the stack lifetime. Weight and volume requirements associated with the use of different fuels are assessed. The annual operation cost consists of fuel consumption and maintenance costs, as well as the application of an environmental tax for CO2 emissions.Different scenarios are proposed to evaluate the impacts of improvements in key parameters on the overall feasibility of the systems. The robustness of the results is evaluated by sensitivity and uncertainty analyses of the key technical and economic parameters used in the model, including, among other parameters, the fuel purchase price, SOFC and battery investment costs, stack lifetime, and interest rate. This research provides a systematic comparison of the techno-economic feasibility of five alternative fuels for cruise ships. The results will aid decision-makers, including shipyards and policymakers, in designing new energy systems with low emissions for maritime applications.