Foraminifera are unicellular organism, which commonly inhabit seafloor. They are often used for paleoenvironmental studies, especially in polar regions. 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 in different parts of fjords. Assemblages in inner and middle parts of fjords seem endemic to South Georgia, but they may become widespread with anticipated warming. Our results are important for interpreting fossil records and monitoring future change.