This paper interrogates the concept of transdisciplinarity, both theoretically and practically, from a perspective of early career researchers (ECRs) in transformative ocean governance research. Aiming to advance research methodologies for future complex sustainability challenges, the paper seeks to illuminate some common uncertainties and challenges surrounding transdisciplinarity from a marine science perspective. Following a literature review on transdisciplinary research, workshops, and a series of surveys, we determine that transdisciplinarity appears to be a concept in search of definition, and that there is a need to explore transdisciplinarity specifically from an ocean research perspective. The paper discusses a number of challenges experienced by ECRs in conducting transdisciplinary research and provides recommendations for both ECRs wishing to undertake more equitable transdisciplinary research and for the UN Decade for Ocean Science to support ECRs in this endeavour (Figure 1). Based on our findings, we interrogate the role of non-academic collaborators in transdisciplinary research and argue that future transdisciplinarity will need to address power imbalances in existing research methods to achieve knowledge co-production, as opposed to knowledge integration.