The aim of this paper is to reveal how the European – Russian political cooperation in the common Baltic Sea Region developed over the last twenty years, ending up at the recently adopted European Union Strategy for the Baltic Sea Region, which excludes Russian participation. This single case study is divided into two well-defined historical periods: starting from the fall of the Berlin Wall until the Eastern Bloc European enlargement and from 2004 to the adoption of the European Union Strategy for the Baltic Sea region in 2009; where comparison and process-tracing methods are applied to connect different variables that matter for clarifying the current state of relations. Furthermore, the analysis is conducted with the help of Constructivist and Neo-Realist theories for two purposes – to achieve stronger scientific explanation and to avoid too loose interpretation of the events. The results show that the Strategy for the Baltic Sea Region is often seen and understood differently by the various political actors, but consequently this leads to a situation in which the role of Russia in the common region remains unclear. When it comes to defining the Russian position today, the Baltic Sea Region provides a good climate for collaboration but so far, the European Union has failed to recognize that the Russian Federation although with a limited access to the sea, remains an actor that should not be ignored. Russia, as well appears confused about its overall foreign policy towards the European Union. Nevertheless, another significant outcome reveals that the levels of regional cooperation have been continuously increasing over the last twenty years, which is an indicator that the Russian presence did not diminish. Finally, the study suggests the European Union Strategy for the Baltic Sea Region is perhaps the beginning of a new tendency towards macro-regional policy development, which will play a future important role in the international relations.