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This study considers how to reconcile different spatial scales to find the best common denominator to be used as an ecosystem-based management unit. For this, two fishery production zones differing ecologically, economically, legally and institutionally were investigated. The first case study is located within French territorial waters, in a MPA created in 2007- the Parc Naturel Marin d'Iroise (PNMI). The second case study, the Bay of Biscay, covers both territorial waters and the French exclusive economic zone. The paper adopts a multidisciplinary approach. Relevant questions concern how marine space is shared between exploited species and fishing fleets, especially the spatial mobility strategies they employ. An assessment of the institutional system established for the PNMI contributes to the discussion of changes in coastal space use. It is obvious that the area in need of protection, defined on the basis of essential fish habitats, does not solely concern the fisheries located within the coastal zone. Experiments conducted by scientists and professionals in the Bay of Biscay provide other key points for the discussion in terms of what institutional frameworks to promote.