This paper presents the simulator SHADYS (‘simulator halieutique de dynamiques spatiales’). SHADYS is a tool devoted to the representation of spatial processes involved in fisheries dynamics. It puts together three fundamental entities in an explicit spatio-temporal way: the environment, the fish populations under consideration and the fishing fleet. It is based on simple, realistic and well identified mechanisms (density-dependent habitat selection, advection and diffusion of a fish population, fishermen search strategy, etc.) implemented by interfacing numerical models with a GIS (geographic information system). As a virtual laboratory, SHADYS allows experiments to be performed in a theoretical world, such experiments being generally impossible to perform in reality. As an illustration, different scenarios of a marine refugia-based management have been explored using the SHADYS simulator. Different simulations are conducted to assess the short-term effects on yield of a marine protected area. It is shown that for diffusive or migratory species, the yield per recruit as a function of the protected surface can reach a maximum. Under this condition, the concept of ‘space overfishing’ is meaningful. Protected areas then behave like ‘sources’ and exploited areas like ‘sinks’. For resident populations, the larger the protected area is, the lower the catches per recruit are. Regarding the spatial distribution of the fishing effort, it is shown that if it is spatially distributed in order to maximize catches, then fishing boats will slowly tend to be distributed all along the boundaries of the protected area.