The recent overexploitation of East Atlantic and Mediterranean bluefin tuna stock has been well documented in the media where it has become the archetype of overfishing and general mis-management. Beyond the public debate, the crisis also highlighted how the interactions between science and management can change through time according to the awareness of the public opinion. To reflect these issues, the history of Atlantic bluefin tuna overfishing is first described. Then, the major uncertainties that undermine the current scientific advice are summarized and the importance of reducing their impacts by improving knowledge and developing robust scientific framework is considered. The study also discusses how uncertainty was used by different lobbies to discredit science-based management. The recent improvement in bluefin tuna stock status following the implementation of the rebuilding plan shows that, despite uncertainty in the scientific advice, the management of a heavily exploited fish stock can be positive when there is a political will. However, optimizing long-term yields of modern fisheries implies good science. The study concludes by advocating for the implementation of a scientific quota that should be part of the management framework to support the scientific advice.