The marine area of Northeast Greenland belongs to the largest national park in the world. Biodiversity assessments and tailored conservation measures often target specific physiographic or oceanographic features of an area for which detailed knowledge on their biological communities is incomplete. This study, therefore, characterizes epibenthic megafauna communities in a priori defined seabed habitats (fjord, shelf, shelf break and slope) and their relationship to environmental conditions in Northeast Greenland waters as a basis for conservation and management planning. Megabenthos was sampled from the Bessel Fjord across the shelf to the upper continental slope between latitudes 74.55°N–79.27°N and longitudes 5.22°W–21.72°W by Campelen and Agassiz trawls at 18 locations (total of 33 samples) at depths between 65 and 1011 m in August 2015 and September 2017. A total of 276 taxa were identified. Gross estimates of abundance ranged from 4 to 854 individuals 1000 m−2 and biomass ranged from 65 to 528 g wet weight 1000 m−2 (2017 only). The phyla Arthropoda and Porifera contributed the most to taxon richness, while Mollusca and Echinodermata were the most abundant, and Echinodermata had the highest biomass of all phyla. Fjord, shelf, shelf break and slope seabed habitats revealed different megafaunal communities that were partly explained by gradients in depth, bottom oxygen concentration, temperature, salinity, and turbidity. The present study provides a current baseline of megabenthos across seabed habitats in Northeast Greenlandic waters and reveals putative connections between Arctic and Atlantic biota.