Methods to assess and manage fisheries have developed considerably over the past three decades; however, their uptake has been restricted due to limited resources in many regions. A key issue for assessing and managing resource-limited fisheries is prioritisation of species and other ecosystem components. We developed a participatory MCDA approach to prioritise species for research in New South Wales, Australia, based on their importance to fisheries management. The approach: (1) structures the decision problem, (2) forces consideration of management objectives at a species level, (3) handles the complex trade-offs generated by multiple fisheries objectives, and (4) balances differences in the perceived importance of management objectives among fisheries managers. Performance scores and attribute weightings for ten management objectives were elicited from two groups of managers focusing on either the commercial or recreational fishing sectors. These values were then used to generate total performance scores for 141 species following Multi-Attribute Value Theory (MAVT). The ordered list facilitates decisions regarding the optimal allocation of limited resources for research in the State. Our approach can be adapted to fisheries in other regions and expanded to include additional ecosystem components.