The benefits of implementing no-take Marine Protected Areas (MPAs) for the conservationof highly migratory species are not easy to assess. They depend on several factors, suchas the fish mobility, fisher behaviour and the area covered by the MPA with respect to thedistribution area of the species to protect. In this study, we explore the simultaneouseffects of MPAs and fishing scenarios on skipjack tuna population dynamics, using thespatially-explicit APECOSM-E model. The model represents the size-structured populationdynamics of skipjack tuna in the Indian Ocean and their dependence on climatic variabilityand exploitation by fisheries. Numerical experiments were run from the beginning ofindustrial fisheries in the early 1980s to the year 2030, considering different scenariosfor the future development of fisheries. These scenarios combined different trends infishing effort and technological development, either assuming a continuous increasefollowing historical trends or a stabilization of these factors at present values. Thesimulations were designed to explore the effects of two MPAs of different size andlocation: the recently established Chagos MPA, and a hypothetical MPA covering a largepart 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 fishershad partial knowledge of the spatial distribution of the skipjack population. The effectsof the two MPAs on the population dynamics, catch and fishing mortality are shown. Ourresults 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 andsucceeded in stabilizing the spawning population. The simulations also showed that theeffect of an MPA depends on the evolution of fisheries and it is therefore important toexplore different fishery scenarios to assess the future benefits of an MPA.