Ecosystem-based management (EBM) is a holistic approach to managing marine environments that can potentially reconcile cross-sectoral conflicts, scale mismatches, and fulfil sustainability objectives. In Aotearoa New Zealand (Aotearoa NZ), the operationalisation of EBM has been uneven; however, a set of principles to guide EBM in Aotearoa NZ provides a useful foundation to enable and enhance its uptake and to support governance approaches that attend to the rights, values, interests, and knowledges of Māori, the Indigenous peoples of Aotearoa. In acknowledging the need to give attention to the governance of marine environments, we apply insights from the ‘relational turn’ in social sciences and sustainability science to explore the ontological and epistemological broadening of ‘governance’ to identify opportunities for alternative forms of governance that accommodate Indigenous ways of knowing. We propose four pou (or enabling conditions) that generate alternatives to governance models underpinned by a ‘modernist’ (dualistic, technocratic) ontology: (i) enacting interactive administrative arrangements; (ii) diversifying knowledge production; (iii) prioritising equity, justice, and social difference; and (iv) recognising interconnections and interconnectedness. Our analysis of seven governance examples exposes evidence of radical and progressive transformations occurring within Aotearoa NZ regarding conceptions of the environment and the role of people in it that could support the wider uptake of EBM. Rather than advocating a ‘perfect model’ of governance for EBM, we find potential in EBM as a strategic approach to managing marine environments because of the synergies with Indigenous and relational ontologies, which lie in the emphasis on interconnectedness, inclusivity, diversity, and relationality.