Fuel cells provide great potential for use on-board ships. Possible fields of application for fuel cells on merchant ships and naval surface ships can generally be summarised as: (1) emergency power supply; (2) electric energy generation, especially in waters and harbours prescribing particular environmental regulations; (3) small power output for propulsion at special operating modes (e.g., very quiet run); and (4) electric power generation for the ship's network and, if required, the propulsion network on vessels equipped with electric power plants (e.g., naval vessels as all-electric ships, AES). In addition, the fuel cell has special importance for realising air-independent propulsion (AIP) on submarines. In the 1970s, the PEMFC system was chosen for AIP on German Navy submarines. Subsequently, this system underwent advanced development up to series maturity including storage on-board of the energy needed. This publication illustrates worldwide activities in this field, taking the various fuel cell system requirements for operation on-board merchant ships, naval surface ships and submarines into consideration. The focus is especially on AIP systems for German submarines because these have already gone into series production. Further developments are discussed which aim to improve the efficiency of hydrogen storage or to generate hydrogen on-board.