Biological diversity, or biodiversity, is high on the international agenda for nature conservation. Marine and coastal ecosystems account for an important share of the biological diversity on Earth. As a consequence many international conventions, European legislation and national laws refer to marine biodiversity. The protection of marine biodiversity is a complex legal issue as it requires consideration of geographic (between land and sea), political (between conservation and exploitation), and economic (between fisheries, tourism, intellectual property and many other sectors) factors. Like Matryoshka dolls, marine biodiversity is a heterogeneous notion difficult to address as one discrete area in the development of policy agendas or juridical frameworks. In the past decade, the EU has been very active in Promoting Integrated Coastal Zone Management and in developing a framework for an Integrated Maritime Policy. This article reviews the status of marine biodiversity in the policy and legal initiatives of the European Union, a challenging issue to both the objectives of conservation and to the concept of integration.