Recent studies have concluded that different water bodies in the ocean can contain different microbial communities. The goal of the present study was to determine if biogeographic patterns are present for aquatic microbes in waters which meet around the South Shetland Islands (SSI), Antarctica. Prokaryotic and eukaryotic marine microbial communities were monitored during the 2007 austral summer by use of polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) of small subunit ribosomal DNA. Hydrographic properties, nutrients and chlorophyll a were also measured. There was an onshore to offshore gradient in temperature, salinity and iron concentration and a unimodal distribution of chlorophyll a concentration in relation to the middle of this gradient that occurred near the SSI. The differences in microbial community structure among stations in the studied area were correlated with both geographical distance and environmental factors. For eukaryotes, the correlation was strongest for environment, whereas it was strongest for geographical distance for the prokaryotes. Eukaryotic and prokaryotic community structures were highly correlated. Surface water from the Weddell Sea had a different community of eukaryotes than the water in the Antarctic Circumpolar Current in the Drake Passage, whereas the prokaryotic community was not significantly different. The area close to the SSI where the 2 water types mix had the highest chlorophyll concentration and significantly different communities of eukaryotes and prokaryotes from both of the inflowing water types. These results suggest that the prokaryote community structure was more affected by productivity than by environmental variables.