Spatial distribution and patchiness of deep sea macrofaunal communities were studied from samples collected in the Rockall Trough, NE Atlantic. In June 2011, two areas, located outside and within the Darwin Mound Special Area of Conservation (SAC), were sampled. Three megacores were deployed in each area at approximately 900 m depth. The two areas, ~ 18 km apart, did not differ in terms of sediment organic matter and percentage of mud content, but small significant differences were found in sediment median grain size and depth. Macrofaunal communities were found to differ significantly, with the difference mostly driven by changes in the abundance of polychaetes, crustaceans and nematodes whilst no significant differences were seen for the other phyla. Whereas overall macrofaunal abundance was higher outside the SAC compared to within, this pattern varies considerably between phyla. Diversity indices showed no significant differences between protected and unprotected sites. Deep-water trawling regularly take place outside the Darwin Mounds SAC whilst the area inside the SAC has been closed to bottom trawling since 2004, and the above distribution patterns are discussed in the context of both environmental and anthropogenic causes.