Abstract Fisheries management has to deal with uncertainty about the genetic composition and the location of fish stocks. If institutions are inert, i.e. unable to adapt to new insights, management may not be effective. This paper analyses fisheries management in Europe which relies on scientific advice feeding into the management decision process. The spatial boundaries of fish stocks define the scientific areas and management areas, which are not necessarily aligned. Even if new scientific information on the stock composition and location leads to changes in scientific areas, the management areas are usually not adjusted. This causes an institutional mismatch which violates the self-imposed good governance principles of the EU. We use the North Sea and the Western horse mackerel stocks to gain some insights in the process of renegotiating new management areas and national fisheries quotas. We find that distributional concerns around allocating quota are a key obstacle for an adjustment of management areas. We suggest to pre-define a transparent mechanism to facilitate adapting management areas to scientific areas.