This paper addresses the problems of institutional changes in governance and the framing of biodiversity conservation policy at the level of the enlarged European Union. The current development of European Union governance has become more complex and multilevel, partially usurping competences from the central state and relying on networks of interconnected actors rather than on a hierarchy dominated and defined by the state. This shift is particularly challenging for biodiversity governance in new member states, where current decision making is still affected by post-socialist relations and massive ongoing institutional changes, often resulting in inefficient institutional designs and over-exploitation of natural resources. The paper offers a cross-country analysis of five Central and Eastern European countries, characterized by different socialist regimes and different transition processes from hierarchical to democratic and market governance. The theoretical basis of the paper is institutional rebuilding in Central and Eastern Europe in the context of the emerging multilevel environmental governance of the EU. The data were collected from desk study research and interviews. The results show that some elements of multilevel governance existed in these countries prior to the transition, but that EU integration empowered lower levels of self-government. The mismatch between the old hierarchical institutions developed under socialism and the new decentralized institutions introduced during the transformation process still persists and is visible. The emergence of multilevel governance with multiple actors' participation is prone to create tensions, but evidence from the countries studied indicates that this is not necessarily a disadvantage. Copyright © 2009 John Wiley & Sons, Ltd and ERP Environment.