One aim of Marine Protected Areas (MPAs) is to protect a representative portion of specific ecosystem functions through spatial closures to extractive practices such as fisheries. Although they usually involve the displacement of fisheries, their design rarely takes into account the effect of that fishery’s displacement on the target fish population. We used a spatially explicit population model of Antarctic toothfish in the Ross Sea region to investigate the effects of a proposed MPA on the status of the toothfish population. This study indicates that the MPA design proposed in 2013 is likely to result in a small increase in the catch limit under existing harvest management rules, as well as a large increase in the area with little depletion of the population and no increase in the area with higher depletion. Such spatial modelling tools can be used to inform MPA planning and compare alternative MPA scenarios. In particular they can assist in quantifying potential effects on the fish population and likely effectiveness of the proposed MPAs to meet some of their conservation goals.