This study compares the macrofaunal communities along two bathymetric transects (1000 – 2500 m water depth) in predominantly ice-covered western (offshore Greenland) and generally ice-free eastern (offshore Svalbard) regions of the Fram Strait. Material was collected using an USNEL 0.25 m2 box corer and all sediment samples were processed through a 500-μm sieve. A total of 1671 organisms from 169 species were found. Densities off Greenland were generally lower than those observed off Svalbard. On both sides of the Fram Strait, density, biomass and biodiversity generally decreased with increasing water depth. An exception was observed at the deepest station off Greenland (2500 m water depth), which was located within the Marginal Ice Zone. At this station, macrofaunal density was elevated (992 ± 281 ind. m−2) compared to the adjacent shallower sampling areas off Greenland (272 ± 208 ind. m−2 to 787 ± 172 ind. m−2) and the deeper stations (2000 and 2500 m water depth) off Svalbard (552 ± 155 ind. m−2 and 756 ± 182 ind. m−2). The most abundant species along both transects was the polychaete Galathowenia fragilis (off Greenland: 288 ind. m−2, off Svalbard: 740 ind. m−2). Sea ice coverage and water depth, as well as the associated food availability at the seafloor, seem to be crucial factors driving the macrofaunal community patterns. A strong pelago-benthic coupling is observed to be typical in Arctic deep-sea ecosystems, and is also confirmed by our study.