The maritime industry leading organization International Maritime Organization (IMO) is bringing more and more restrictive and effective rules on reducing greenhouse gas and air polluting emissions since the significant portion of the greenhouse gas emissions in the world are caused by commercial vessels. Therefore, an alternative energy source is seeking by maritime industry and fuel cells can play a major role in converting such energy sources into electrical energy. The aim of this study is to compare commercial fuel cell types that can be used in merchant ships and a maximum of 5MW main engine power is considered due to the limited power output of fuel cells. The environmental and economical performances of fuel cell types were compared and criterions' weightings were found according to expert points using the analytic hierarchy process. A final comparison table is formed giving evaluation points for each fuel cell type and weighting for each criterion depending on their importance in the maritime industry. Fuel cells are ranked by eight different criteria and according to experts, safety is the most important criterion and then followed by emissions, efficiency, cost, lifetime, power output, fuel type, and size, respectively. Among seven different fuel cell types; proton exchange membrane, alkaline, phosphoric acid, diesel oil using molten carbonate, liquefied natural gas using molten carbonate, diesel oil using solid oxide and liquefied natural gas using solid oxide fuel cells, the first three places are formed by diesel oil using molten carbonate fuel cell, proton exchange membrane fuel cell and diesel oil using solid oxide fuel cell which are received 4.053, 4.044 and 3.969 respectively from the total point 5.000. As a result, diesel oil using molten carbonate fuel cell, which takes place with a slight margin from proton exchange membrane fuel cell, has been found as the most suitable fuel cell type for ships. This study highlights that despite strict emission regulations, as a fuel, diesel oil is still a strong fuel option for ships with different energy conversion units like fuel cells. (c) 2020 Elsevier Ltd. All rights reserved.