We studied foraminifera living in the fjords of South Georgia, a sub-Antarctic island sensitive to climate change. As conditions in water and on the seafloor vary, different associations of these microorganisms dominate far inside, in the middle, and near fjord openings. Assemblages in inner and middle parts of fjords are specific to South Georgia, but they may become widespread with anticipated warming. These results are important for interpretating fossil records and monitoring future change.