There is broad agreement that marine spatial planning (MSP) should incorporate transboundary considerations, reflecting the cross-border nature of marine and coastal ecosystem dynamics and maritime resources and activities. This is recognised in the European Union’s recent legislation on MSP, and experience in transboundary approaches is developing through official processes and pilot studies. However, differences between institutional systems, priorities and practices may not easily be overcome in transboundary initiatives. This requires a stronger focus on understanding the governance frameworks within which MSP operates and fostering interlinkages between them. This article discusses a European-funded project in which emphasis was placed on joint-working in every aspect, based on principles of equity and mutual trust. This led to the development of inter-relations, not just of the geographies and maritime resources and activities of the marine areas concerned, but also of the systems of data management, governance and policy-making and of the participants involved as officials or stakeholders, including their means and cultures of exchange. It is suggested that transboundary initiatives in MSP would benefit by complementing current resource management-focused understandings with governance and policy-related perspectives, drawing on experience in other fields of territorial cooperation.