Bottom trawling causes chronic and widespread disturbance to the seabed in shallow shelf seas and could lead to changes in the trophic structure and function of benthic communities, with important implications for the processing of primary production and the wider functioning of the marine ecosystem. We studied the effects of bottom trawling on the trophic structure of infaunal and epifaunal benthic communities in 2 regions (Silver Pit and Hills) of the central North Sea. Within each region, we quantified long-term (over 5 yr) differences in trawling disturbance at a series of sites (using sightings data from fishery protection flights), and related this to differences in the biomass and trophic structure of the benthic community. There were 27- and 10-fold differences in levels of beam trawl disturbance among the Silver Pit and Hills sites respectively, and we estimated that the frequency with which the entire area of the sites was trawled ranged from 0.2 to 6.5 times yr-1 in the Silver Pit and 0.2 to 2.3 times yr-1 in the Hills. The impacts of-fishing were most pronounced in the Silver Pit region, where the range of trawling disturbance was greater. Infaunal and epifaunal biomass decreased significantly with trawling disturbance. Within the infauna, there were highly significant decreases in the biomass of bivalves and spatangoids (burrowing sea-urchins) but no significant change in polychaetes. Relationships between trophic level (estimated using nitrogen stable isotope composition, d15N) and body mass (as log2 size classes) were rarely significant, implying that the larger individuals in this community did not consistently prey on the smaller ones. For epifauna, the relationships were significant, but the slopes or intercepts of the fitted linear regressions were not significantly related to trawling disturbance. Moreover, mean d15N of the sampled infaunal and epifaunal communities were remarkably consistent across sites and not significantly related to trawling disturbance. Our results suggest that chronic trawling disturbance led to dramatic reductions in the biomass of infauna and epifauna, but these reductions were not reflected in changes to the mean trophic level of the community, or the relationships between the trophic levels of different sizes of epifauna. The trophic structure of intensively trawled benthic invertebrate communities may be a robust feature of this marine ecosystem, thus ensuring the efficient processing of production within those animals that have sufficiently high intrinsic rates of population increase to withstand the levels of mortality imposed by trawling.