The marine research vessel (RV) Dr Fridtjof Nansen is a familiar visitor to the coastal waters of developing countries around the world. Since its first expedition in 1975, to survey fish abundance in an upwelling region of the Western Indian Ocean, the Nansen has returned to this “least known” of the world’s oceans numerous times. The Nansen surveys first focussed on finding new fish resources, but expanded later to sample whole ecosystems and complex oceanographic processes. Over time, the charismatic Nansen has become a “flagship” for a multitude of resource and capacity development initiatives, extending far beyond surveys at sea. Along with the Nansen surveys, these initiatives form part of the broader Nansen Programme (after 2006 the EAF-Nansen Project), a cooperative development programme shared by the Norwegian government and the FAO. We showcase the research done to discover new resources, and to decipher the linkages between fish abundance, ocean productivity, and the oceanographic processes that maintain ecosystems. The review shows the enduring impact of the Nansen Programme on fisheries and marine science in the Western Indian Ocean, and highlights crucial gaps in information. Based on past experience, recommendations for future work are made. The review coincides with the transition from the EAF-Nansen Project (2006–2016) to the new and enlarged EAF-Nansen Programme in 2017, and with the launch of a new ship, the third RV Dr Fridtjof Nansen, better-equipped and technologically more advanced than its predecessors.