During the austral summer of 2008, we carried out a high resolution survey of the microplankton communities along a south to north transect covering a range of environments across the Scotia Sea, Southern Ocean; high and low productivity, sea-ice to open water conditions, and over a number of oceanographic fronts and bathymetric features. Cluster analysis revealed five distinct communities that were geographically constrained by physical features of bathymetry and fronts. From south to north the communities were: (1) the South Orkney group, a mixed community of naked dinoflagellates and heavily silicified diatoms, (2) southern Scotia Sea, a mixed community of cyptophytes and naked dinoflagellates, (3) central Scotia Sea, dominated by naked dinoflagellates, (4) southwest of the island of South Georgia, lightly silicified diatoms and naked dinoflagellates (5) northwest of South Georgia, dominated by diatoms. Data from a previous summer cruise (2003) to the Scotia Sea followed a similar pattern of community distribution. MODIS images, Chlorophyll a and macronutrient deficits revealed dense phytoplankton blooms occurred around the island of South Georgia, were absent near the ice edge and in the central Scotia Sea and were moderate in the southern Scotia Sea. Using these environmental factors, together with community composition, we propose that south of the Southern Antarctic Circumpolar Current Front, biogenic silica is preferentially exported and north of the front, in the vicinity of South Georgia, carbon is exported to depth.