Now, there are two big issues threatening global society, which are the depletion of fossil fuels and the environmental disruption. Therefore, marine diesel engine, taking up over 95% share of the marine power market, has met the environmental and economical problems, too. These problems have caused a necessity of new, alternative power systems in ships and fuel cell systems has been playing a central role as one of the alternatives. This paper analyzes the characteristics of marine fuel cell systems, R&D trends of advanced countries, and mapping out R&D strategy of Korea.