The ocean ecosystems around the west Antarctic Peninsula and South Georgia are two of the best described regional ecosystems of the Southern Ocean. They therefore provide a useful basis for developing comparative analyses of ocean ecosystems around the Antarctic. There are clear and expected differences in seasonality and species composition between the two ecosystems, but these mask an underlying similarity in ecosystem structure and function. This similarity results from the two ecosystems being part of a continuum, from more ice covered regions in the south to open water regions in the north. Within this continuum the major factors affecting ecosystem structure and function are the sea ice, the biogeochemical conditions and the connectivity generated by the flow of the Antarctic Circumpolar Current. Antarctic krill are central to the food web in both ecosystems, but the other species of plankton and predators present are different. These different species provide alternative pathways of energy transfer from primary production to the highest trophic levels. The relative dominance of these species can provide indicators of change in ecosystem structure and function. Both ecosystems are changing as a result of physically and biologically driven processes, and the ecological responses being observed are complex and variable across different species and within the two regions. Species in parts of the northern Antarctic Peninsula are being replaced by species that currently dominate farther north in more oceanic areas such as at South Georgia. The similarity of structure and strong connectivity, mean that projections of future change will require generic models of these ecosystems that can encompass changes in structure and function within a connected continuum from ice covered to open water in winter.