A method to study bacterioplankton community structure in Antarctic freshwater lake samples is described. Small samples (between 300 and 1000 ml) taken in remote field locations were used for crude DNA extraction, followed by PCR amplification of 16S rRNA gene fragments using group-specific primers. The amplification products of the PCR reaction were then separated using denaturing gradient gel electrophoresis to produce a profile of the bacterioplankton community. Whilst the technique is only semi-quantitative, it readily differentiated communities from lakes of different trophic status and from vertical profiles within different lake types. The method offers a sensitive tool for screening and monitoring Antarctic freshwater environments as a precursor and adjunct to more detailed studies.