The ecosystem-based management (EBM) philosophy draws upon the principle that holistic understanding of the system to be governed needs to guide the decision-making process. However, empirical evidence is growing that knowledge integration is still a main bottleneck for EBM decision-makers. This paper argues that transdisciplinary knowledge management (TKM) is a key competence in achieving knowledge integration, while simultaneously it represents an underdeveloped research area in EBM if understood as a process of human interaction. Based on a literature review, this article summarizes and reflects upon the most recent development in the field of TKM. The paper presents a detailed definition and in-depth description of TKM as a process of human interaction and a diversity of organizational structures that effectuate TKM. Theoretically discussed premises are furthermore illuminated and evaluated by a case study that exemplifies pro-active development and implementation of TKM. Deviating case observations are presented as novel contributions to the field. They suggest new ideas and inspiration for future EBM research and policy agendas.