Knowledge co-production has become part of an evolution of participatory and transdisciplinary research approaches that are increasingly important for achieving sustainability. To effectively involve the most appropriate stakeholders there is a need for engagement and increasing prominence of stakeholders in environmental management and governance processes. The paper aims at developing and testing a methodology for stratifying stakeholders by (i) classifying organisations involved in coastal and ocean governance by their agency, and (ii) grouping them into organisational archetypes for representation and selection in research processes. Agency was measured by the three dimensions of scale, resources, and power. Each dimension was further elaborated as a set of indicators. The methodology is applied in the context of a research project set in Algoa Bay, South Africa. The stratification of organisations enabled the research team to gain a better understanding of the stakeholder landscape of organisational agency, and thus identify the most relevant stakeholder with which to engage. The use of a hierarchical cluster analysis identified five organisational archetypes in relation to ocean and coastal governance in Algoa Bay. The methodology used in this study proposes an informed and intentional approach to create the conditions under which the co-production of and participation in research processes can take place.