The Filchner-Rønne Outflow System (FROS) in the southernmost Weddell Sea is unique, as sea ice persists longer there than in any other region in the Southern Ocean (SO), strongly determining the ecological processes in the water column and on the seabed. It consists of the deep Filchner Trough (> 1000 m in depth), which conducts water into and from the Filchner-Rønne Ice Shelf and separates two high-Antarctic shelf regions east and west of it. As the system is situated in a remote high-latitude area rather difficult to access, which greatly hampers scientific studies in the region, the knowledge about ecological processes in the FROS was scarce. However, during two cruises of R/V Polarstern in 2013/14 and 2015/16 field campaigns were performed, which united a multidisciplinary community of scientists intensely collaborating with a common overarching approach to study the FROS. Novel data was gathered by means of corers (multi-corer and multi-grab) and seabed imagery to investigate both infaunal and epifaunal seabed assemblages. First analyses indicated that the macro- and megabenthos on the shelf west of the Filchner Trough was clearly poorer in both abundance and diversity than that at eastern stations. Based on this evidence, we hypothesize that the western and eastern Filchner shelf regions are contrasting ecological systems, characterized by pronouncedly different environmental conditions and distinct benthic communities. We hypothesize further that this difference is primarily due to the contrasting sea-ice regimes, with almost permanent ice cover in the western region vs. the formation of a recurrent summer polynya in the east. As a result, the western system lacks the typical high-Antarctic summer conditions, such as occurrence of wide open-water areas, enhanced light regime, upper water-column stratification triggering phytoplankton blooms, high primary production and particle fluxes, and, hence, strong pelagic-benthic coupling and enhanced food supply to the benthos. In addition, this east-west contrast in the general environmental setting is sustained by the isolating effect of the regional oceanographic current pattern, impeding advective exchange processes (organic matter, larvae, propagules) between the two shelf regions across the trough. As there was evidence from bathymetric as well as seabed imaging data that iceberg scouring likewise impacts both the eastern and western shelf, we further hypothesize that this process, which is generally of high ecological significance for SO shelf benthic systems, does not explain the striking difference in epibenthic community structures. However, as the available evidence is based on admittedly rather few point-type and snapshot-like data, further samples are required to rigorously test those hypotheses.