Global warming and other environmental concerns drive the search for alternative fuels in international shipping. A life-cycle analysis (LCA) can be utilized to assess the environmental impact of different fuels, thereby enabling the identification of the most sustainable alternative among the candidate fuels. However, most LCA studies do not consider marginal emissions, which are important when predicting the effects of large-scale fuel transitions. The research purpose of this study was to assess the marginal emissions of several currently available marine fuels to facilitate the identification of the most promising marine fuel. Thus, marginal and average emissions for eight marine fuels (high-sulfur fuel oil, very-low-sulfur fuel oil, marine gas oil, liquified natural gas, biomethane, biomethanol, fossil methanol, and hydro-treated vegetable oil) were compared in terms of their environmental impact. Non-intuitively, the results indicate that biofuels exhibit equally or higher marginal greenhouse gas emissions than conventionally used fuel oils (162–270 versus 148–174 kg CO2/MJ propulsion), despite their significantly lower average emissions (19–73 vs. 169–175 kg CO2/MJ). This discrepancy is attributed to the current limited availability of climate-efficient biofuels. Consequently, a large-scale shift to biofuels cannot presently yield substantial reductions in the shipping industry’s climate impact. Additional measures, such as optimized trading routes, more energy-efficient ships, and research on more climate-friendly biofuels and electro-fuels, are thus required to significantly reduce the climate footprint of shipping.