The benefits of implementing no-take Marine Protected Areas (MPAs) for the conservation of highly migratory species are not easy to assess. They depend on several factors, such as the fish mobility, fisher behaviour and the area covered by the MPA with respect to the distribution area of the species to protect. In this study, we explore the simultaneous effects of MPAs and fishing scenarios on skipjack tuna population dynamics, using the spatially-explicit APECOSM-E model. The model represents the size-structured population dynamics of skipjack tuna in the Indian Ocean and their dependence on climatic variability and exploitation by fisheries. Numerical experiments were run from the beginning of industrial fisheries in the early 1980s to the year 2030, considering different scenarios for the future development of fisheries. These scenarios combined different trends in fishing effort and technological development, either assuming a continuous increase following historical trends or a stabilization of these factors at present values. The simulations were designed to explore the effects of two MPAs of different size and location: the recently established Chagos MPA, and a hypothetical MPA covering a large part of the Western Indian Ocean, where most of the skipjack catches are presently made. We modelled the redistribution of fishing effort around the MPAs assuming that the fishers had partial knowledge of the spatial distribution of the skipjack population. The effects of the two MPAs on the population dynamics, catch and fishing mortality are shown. Our results revealed a very minor effect of the Chagos MPA on the skipjack tuna population, while the Western Indian Ocean MPA had an important impact on the fishing mortality and succeeded in stabilizing the spawning population. The simulations also showed that the effect of an MPA depends on the evolution of fisheries and it is therefore important to explore different fishery scenarios to assess the future benefits of an MPA. [ABSTRACT FROM AUTHOR]