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The Adriatic and Ionian Region is an important area for both strategic maritime development and biodiversity conservation in the European Union (EU). However, given that both EU and non‐EU countries border the sea, multiple legal and regulatory frameworks operate at different scales, which can hinder the coordinated long‐term sustainable development of the region. Transboundary marine spatial planning can help overcome these challenges by building consensus on planning objectives and making the trade‐offs between biodiversity conservation and its influence on economically important sectors more explicit. We address this challenge by developing and testing 4 spatial prioritization strategies with the decision‐support tool Marxan, which meets targets for biodiversity conservation while minimizing impacts to users. We evaluated these strategies in terms of how priority areas shift under different scales of …