Pockmarks are concave depressions on the sea bottom produced by fluid escape from subaqueous sediments which can be found worldwide in muddy and silt/clay sediments. Due to their morphological and geochemical characteristics, certain pockmarks play an important role in structuring benthic communities, and consequently, they have been proposed to be protected. The present research provides a characterisation of the benthic macrofauna composition in pockmark fields in the southeaster Bay of Biscay. A total of 11 samples were acquired in and close to pockmarks covering a range of depths of 414–992 m. The survey strategy considered the acquisition of one sample inside of each of the selected pockmarks and another sample near, but out of them. Collected macrofaunal organisms were identified at lowest taxonomical level (species) when possible, structural parameters were calculated and a hierarchical cluster analysis carried out with species data. Species density, biomass, richness, diversity and evenness were found to be higher in samples collected inside pockmarks in comparison to samples obtained outside but not statistically significant. This could be explained by the inactivity of the studied pockmarks, which do not offer/generate a particular environment with unusual characteristics that limit or enhance the development of specific species/groups with special traits.