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Ship emissions reduction targets are pushing the maritime industry towards more sustainable and cleaner energy solutions. Marine fuels play a major role in this because of the emissions resulting from the combustion process associated with the prime mover(s), therefore, one of the technical solutions is to replace conventional marine fuels with cleaner fuels. Hence the aim of this study is to undertake environmental, technical, and economic analysis of alternative fuels to reduce the environmental footprint and lifetime costs of the long-distance shipping sector. As a case study, an ultra large container ship operating on the East-West trade route has been considered, and the analysis focus ed on natural gas and methanol as alternative fuels. This study adopted three approaches : environmental, technical, and economic methods to compare the alternative fuels with the conventional ones. The results showed that a dual-fuel engine operated by natural gas will reduce CO2, SOx, and NOx emissions by 28%, 98% and 85%, respectively , when compared with emission values for a diesel-powered engine. Furthermore, the reduction percentages reach 7%, 95% and 80% when using a dual-fuel engine operated by methanol, respectively. The proposed dual-fuel engines will improve the ship energy efficiency index by 26% and 7%, respectively. The study shows that methanol is the most economical alternative fuel for this container ship, replacing diesel with methanol, leads to a power system that is only 30% more expensive than the existing one. The analysis confirms that the cost of fuel has a major effect on the ship’s life cycle cost and that by reducing the fuel costs, the costs of the power system become more acceptable.