Molecular biology tools are widely used to monitor the modifications of bacterial communities and evaluate their activities. However, the application of nucleic acid-based tools has been hindered by the lack of available sequences for environmentally relevant functional genes. We describe here a protocol for random arbitrarily primed PCR (RAP-PCR) and differential display (DD), powerful techniques for revealing specific differences between two RNA populations including the unknown part of functional transcripts. They allow the identification of new functional genes induced in response to the presence of pollutants without prior knowledge of gene sequences.