The effects of decreasing bottom depth on the vertical migrating mesopelagic fish community was investigated at three shallow topographic features in the NE Atlantic. For this purpose the fish assemblage was sampled over three different bathymetric depth zones by stratified horizontal midwater tows. Our results showed a reduced mesopelagic fish biomass, species number and diversity above the flanks of Atlantis Seamount and Great Meteor Seamount compared to the surrounding oceanic deep water. There was no evidence for the existence of a seamount associated mesopelagic community at both study areas. The mesopelagic fish assemblages sampled above the seamount slopes is best described as a thinned out oceanic community. Over the plateaus of both seamounts we observed an almost complete lack of mesopelagic fish species. The truncation of the vertical migration range by shallow bottom topography and enhanced predation effects are presumed to be the main reasons for the observed gaps in mesopelagic fish abundance above the plateaus of both seamounts. The third investigated submarine feature, a pinnacle like structure associated with the Mid-Atlantic Ridge, showed no markedly effect in regard to biomass distribution and diversity on the mesopelagic fish community. This probably due to the much smaller and deeper summit area of this submarine feature in comparison to the studied table seamounts.