The ecological network of Natura 2000, an European Union (EU) initiative to halt biodiversity loss across Europe, has dominated biodiversity governance in the new EU member states in recent years, as implementation was a condition of accession. Non-governmental organizations (NGOs) have generally assisted Natura 2000 implementation. In two Central and Eastern European countries (Poland and Hungary), NGOs became involved in different ways; this paper seeks to analyse and explain these national differences by researching the theoretical background of policy networks and advocacy coalitions in both countries. In Hungary, NGOs worked closely with governmental authorities and contributed significantly to site selection. In Poland, NGOs initially opposed government plans, but later moved toward close cooperation with public institutions; this resulted in a significant expansion in the area and number of designated Natura 2000 sites. In both countries, NGO influence increased during the Natura 2000 process owing to the establishment of multi-level policy networks with the European Commission and public institutions, based on resource dependencies and shared beliefs. In post-socialist countries, the progression from government-monopolized biodiversity conservation implies a growing importance and contribution of NGOs, and their ability to use resources appropriately in the new governance contexts.