The primary objective of the paper is to address the problems of institutional changes in governance and biodiversity conservation policy framing at the level of the enlarged European Union. The paper offers a cross-country analysis in several Central and Eastern European countries in the process of transition from hierarchical to democratic and market governance. These are three new EU member states: Poland, the Czech Republic, and Slovakia as well as countries characterized by different socialist regimes and transition histories, such as Serbia, and the Belarus. The theoretical basis for the paper is the institutional rebuilding in Central and Eastern Europe in the context of emerging multilevel environmental governance of the EU. The results show that the decentralization together with the increasing role of nonstate actors results in cross-scale coordination and information problems in all the countries. The appearance of formal and informal institutions operating at multiple levels and involving a multitude of groups of actors is an example of multilevel governance that is likely to prove more resilient than the traditional hierarchical governance.