The exhaust gas emission from marine diesel engines is one of the major environmental issues. The authors focus the use of photovoltaic energy for the electric power system on marine ships. This paper proposes an operation method of a photovoltaic/diesel hybrid generating system for a small ship in consideration of the fluctuating photovoltaic power due to solar radiation. The aim of the proposed operation method is to minimize the fuel consumption and storage capacity of the battery. The validity of the proposed control method is shown by the numerical simulation based on the experimental data of the photovoltaic system.