The organisms living on and in the sea floor, the benthos, represent an important ecological group. Although some (shellfish) have an economic value, most do not, and so little long-term data are available. We have identified three sources of historic benthic data for the North Sea, a regional sea that has been subjected to multiple human impacts for at least several hundred years. Each dataset has its limitations, but by their use together some issues emerge. Wider community shifts were observed in the shorter term and a number of extirpations at the scale of the North Sea were seen over longer time scales. The extirpated taxa share a number of characteristics consistent with an effect of fisheries such as fragile morphology. We must concentrate now on furthering our understanding of the ecological significance of shifts in dominance of particular functional units and protecting those habitats and species most vulnerable to fisheries-driven extirpation.