Taxonomic composition and ecological structure of benthic communities of the southern part of St. Anna Trough were investigated during the 54th and 59th cruises of RV Akademik Mstislav Keldysh. Material was collected using Sigsbee trawl at 10 stations arranged in two transects (depth range 57–554 m). It was shown that benthic communities of the western arm of the St. Anna Trough differ considerably from the communities of the eastern arm. The western arm communities develop under the influence of active near-bottom hydrodynamics in conditions of rugged topography and a coarse-grained sediment or hard substrate. The wastern arm of the trough is characterized by the predomination of the soft sediment, smooth topography, and weak currents. In the western arm of the trough the influence of the Barents Sea fauna is traced down to the edge of the internal shelf (about 150 m depth). The community of the eastern arm of the trough situated out from the direct influence of the Barents Sea waters represents a continuation of the Ophiocten sericeum community, typical for external Kara Sea shelf. With increasing depth, Ophiopleura borealis becomes the dominant species of the community. In the greatest explored depths some deep-water High-Arctic species, such as echinoids Pourtalesia jeffreysi, were observed. The major factors determining the distribution of benthic communities in the investigated area are the microrelief pattern, the sediment structure, and near-bottom hydrodynamics.