Pockmarks are one of the most obvious and abundant structural features of the North Sea seabed, yet their influence on fauna is virtually unknown. We report the distribution of benthic megafaunal assemblages in and around four “pockmark complexes” in the North Sea to determine the structure of megafaunal communities inside pockmarks and whether these ubiquitous topographical features acted as refuges against trawling and other disturbances. The study focuses on the large central pockmarks in each of the pockmark complexes. These large pockmarks had depths of around 10 m and diameters of 160-235 m. Remotely operated vehicle video transects showed that megafauna increased in abundance, species richness, and diversity from outside (background seabed) toward the center of the pockmarks. The number of taxa present in the center of pockmarks was approximately double those of similar surrounding areas, and the centers had almost an order of magnitude more individuals than outside. Carbonate rocks were found in the centers of all the pockmarks and may be indicative of their formation (past methane seeps). These rocks also provide novel habitat to fauna: a complex hard substrate for colonization and shelter in an otherwise homogeneous soft sediment environment. Habitat enrichment and morphological protection are suggested to be the main reasons for the increased faunal abundance and species richness. Indeed, despite fishing data showing the area to be intensively disturbed, large slow-growing (old) and vulnerable species, such as gorgonian corals, were found in the center of the pockmarks. Pockmarks may offer important refuges from trawling activity.