Successful public conservation policies at various governmental levels have increased some populations of protected species to the extent that they are causing damage to human activities, like fisheries. As a reaction public authorities are developing biodiversity reconciliation policies. Finland and Germany have both created reconciliation policies for the conflicts between nature conservation and fisheries including a package of measures like management of population, support of technical measures and various types of compensation payments. All these measures are affected by European policy and law, though no special reconciliation policy has been adopted at European level. This article explores the options European regulation offers and the restrictions it imposes on Member States. Based on experiences with German and Finnish biodiversity reconciliation policies, the interrelationship between European and national regulation is elaborated, leading to suggestions for better coordination of reconciliation policies between different governmental levels.