The eastern side of the Fram Strait is significantly influenced by the northern-bound warm West Spitsbergen Current (WSC) whereas the western side is affected by the cold and less saline East Greenland Current (EGC) flowing in a southerly direction. These current regimes are major factors in regulating the ice coverage in the Fram strait. In turn, this coverage plays an important role in determining the flux of food to the seafloor. The objective of this study is to compare the macrofaunal community structure along two bathymetrical transects (1000 to 2500 m) at the LTER (Long-Term Ecology Research) observatory HAUSGARTEN; one transect in the eastern Fram Strait and a second in the western region of the strait. Material was collected during RV Polarstern expedition PS99.2 in June/July 2016 using an USNEL box corer with a sampling area of 0.25 m². Samples were processed through a 500 μm mesh size sieve. Results showed a higher macrofaunal density at the stations located in the eastern Fram Strait. Species richness, biomass and biodiversity showed a trend to decrease with increase in depth on both sides of the strait. An exception was observed at one station at 2500 m depth off Greenland, which was located in the marginal ice zone. Densities and species diversity were higher at this station than at the adjacent shallower sampling locations. Polychaetes were the generally most abundant taxon, followed by crustaceans and molluscs. Species composition along the two bathymetrical transects on both sides of the strait clearly changed with increasing depth. Sea ice coverage and depth, with the associated variabilities in food quality and quantity reaching the seafloor seemed to be crucial factors driving community patterns.