Bacterial community composition during summer was analysed in surface and bottom waters of the oligotrophic shallow (4.5 m) Lake Limnopolar (Livingston Island, South Shetland Islands, Antarctica), using 16S rRNA gene clone libraries and sequencing. Up to 61% of the 16S rDNA sequences found were closely related to sequences retrieved from lakes, glaciers or polar systems. The distribution of these sequences was not homogeneous, with vertical differences found in both bacterial taxa composition and isolation source of the closest match from GenBank. In the surface sample 86% of the sequences were related to bacteria found in soils, seawater or gut microbiota, probably explained by waterborne transport from the catchment, by wind through sea sprays, or local bird activity. Conversely, in the deep samples, 95% of the sequences were closer to bacteria typically described for lakes, glaciers or polar systems. The presence of benthic mosses covering the bottom of the lake favours a more stable deep layer leading to the existence of this biological heterogeneity through the water column, although the lake does not show physical-chemical stratification in summer. This study illustrates a strong influence of external factors on the microbial ecology of this model Antarctic lake.