The structure of North Sea benthic invertebrate and fish communities is an important indicator of anthropogenic and environmental impacts. Although North Sea fish stocks are monitored regularly, benthic fauna are not. Here, we report the results of a survey carried out in 2000, in which five nations sampled the epibenthic and fish fauna at 270 stations throughout the North Sea. The aim of the survey was to investigate the diversity and community structure of epibenthic and fish communities and to identify relationships with environmental factors, including the frequency of commercial otter and beam trawling disturbance. Epibenthic species diversity was lower in the southern North Sea than in central and northern areas. Fish, conversely, were more diverse in the south. The 50 m, 100 m and 200 m depth contours broadly defined the boundaries of benthic and fish communities. The abundance of epibenthos of the southern North Sea was dominated by free-living species, whilst north of the 50 m contour sessile species prevailed. A hybrid area, with sessile species typical of the north and free-living species characteristic of the south, was found off the Norfolk and Flamborough coast stretching towards the Dogger Bank. Large-scale hydrodynamic phenomena were most likely to be responsible for the main divisions between communities, especially the boundary between mixed and stratified water masses. However, bottom temperature, sediment parameters and beam trawling were closely correlated with species richness and diversity, as well as community patterns, and may modify regional species composition. Our study shows that effective large-scale sampling of benthic communities can be conducted during existing fisheries surveys. Since annual fisheries surveys are conducted throughout the northeast Atlantic shelf seas, concurrent benthic surveys would allow benthic sampling on unprecedented spatial and temporal scales. The samples would help to monitor the environmental impacts of trawling disturbance, climate change, pollution and other natural and anthropogenic factors.