During the last 50 yrs (at least), fishery science and fisheries management have undergone a long process of co-evolution with periods of crisis in their relationship with society. The current one, following the last resources collapse and public recognition of the high failure rate of conventional management, is therefore not new but, once again, it questions the role and responsibility of fisheries science. This relationship is blotted with issues regarding the specific role of science in promoting sustainability; the use of science in decision-making or in advocacy; the science and management crisis; the relationship between crises and institutional evolution; the ongoing trend from consensus to polarization and litigation; the quality and problems of communication; the cost and affordability of science; the lack of clear management objectives; and the use of traditional knowledge. Fishery science is facing three new concepts which, while having significant scientific requirements, originate from the general societal debate on environmental conservation, uncertainty, and societal risks. These pose new challenges to fishery science in its contribution to the implementation of the precautionary approach, the development of sustainable development reference systems (SDRSs) with indicators and reference points, and the scientific basis for ecosystem-based fisheries management. Structuring the research framework, these related or nested concepts lay the basis for a much more broadly based scientific approach to development and management, as well as improved decision-making. They also require scientists to better understand their role and that of the other stakeholders and society in decision-making in a holistic and uncertain context.