Despite the increasing attention given to marine spatial planning and the widely acknowledged need for transnational policy coordination, regional coherence has not yet improved a great deal in the Baltic Sea region. Therefore, the main objectives in this article are: (a) to map existing governance structures at all levels that influence how domestic marine spatial planning policy strategies are formed, (b) to identify specific challenges to improved regional cooperation and coordination, and (c) to discuss possible remedies. Based on data from indepth case studies carried out in the BONUS BALTSPACE research project, it is shown that, despite the shared goal of sustainability and efficient resource use in relevant EU Directives, action plans and other policy instruments, domestic plans are emerging in diverse ways, mainly reflecting varying domestic administrative structures, sectoral interests, political prioritisations, and handling of potentially conflicting policy objectives. A fruitful distinction can be made between, on the one hand, regulatory institutions and structures above the state level where decision-making mechanisms are typically grounded in consensual regimes and, on the other hand, bilateral, issue-specific collaboration, typically between adjacent countries. It is argued that, to improve overall marine spatial planning governance, these two governance components need to be brought together to improve consistency between regional alignment and to enhance opportunities for countries to collaborate at lower levels. Issue-specific transnational working groups or workshops can be one way to identify and act upon such potential synergies.