Amphipoda belong to enormously diverse benthic invertebrate groups in the Southern Ocean, playing a very important role in the Antarctic communities. However, in the majority of ecological studies they are identified only to the order level. Rare ecological studies, where amphipods were identified to the species level, concern mainly shallow sublittoral. There is also poor knowledge about the environmental features that are important in the habitat selection by these crustaceans. The aims of this study were to recognize and describe the soft bottom sublittoral amphipod assemblages of the Antarctic fjord and observe the habitat preferences of dominant species. Additionally, we investigated the usefulness of surrogacy methods in the description of amphipod assemblages. The series of 101 quantitative samples from wide depth range (25–502 m) from Admiralty Bay were studied. The cluster analysis allowed to distinguish four assemblages representing: shallow sublittoral (A), middle sublittoral (B) and deep sublittoral (C) of central basin of the bay and Ezcurra Inlet (D) fauna. The study of habitat preferences led to the recognition of the species whose distribution depended on the depth and type of the sediment. The first group encompassed shallow water species characteristic of assemblage (A). The second set of species was related to the presence of colonial organisms identifying the assemblage (B). Third group of deep water species represented assemblage C, while the group of species preferring fine-grained sediments was found in assemblage D. The surrogacy analysis demonstrated low usefulness of this method in the description of Antarctic amphipod assemblages in non-disturbed areas.