To reduce the pollutant emissions in the naval sector, the use of alternative fuels and new power generator systems are both promising solutions. In this study, the feasibility of replacing a pleasure boat Auxiliary Power Unit (APU) with a hybrid solution is studied from the economic and technical points of view. Several power generation technologies and layouts are considered. Many configurations were investigated, from hybrid battery/diesel generator to innovative layouts including fuel cell with onboard Liquified Natural Gas (LNG) reforming for hydrogen production. Since hybrid APUs may yield significant advantages in terms of both environmental and noise pollution, the opportunity of operating the system for several hours without powering up the traditional generators is also considered. For each configuration, CO2 and NOx emissions, purchasing and operating costs, as well as weight and volume, are estimated. Emissions may be reduced up to 20 % and 60 % for CO2 and NOx, respectively, and fuel cost reductions up to 35 % may be achieved.