In recent decades there has been steady progress towards a risk-based management approach for fisheries. An important first step in a risk analysis framework is scoping to identify, describe and catalog the sources of uncertainty that might have an impact on a fishery. This paper introduces a methodology based on a range of tools to formalize the process of elicitation of uncertainties, from both experts and stakeholders, for the International Commission for the Conservation of Atlantic Tunas (ICCAT). ICCAT is a regional fisheries management organization responsible for the conservation of tunas and other highly migratory fish in the Atlantic Ocean and its adjacent seas. The aim of the elicitation was to identify and prioritize uncertainties for inclusion in Operating Models for Management Strategy Evaluation (MSE). The tool presented in this paper supports the qualitative prioritization of uncertainties, while also visualizing the degree of consensus among stakeholders on particular issues. Perceptions of uncertainty in fisheries often vary widely among scientists, industry and other interest groups, so tools that can facilitate inclusion and representation of different opinions are useful where decision-making depends on broad agreement and more generally, where effective management depends on commitment from stakeholders.