AIMS: We performed a preliminary assessment of the eukaryotic 18S rDNA diversity present in finished drinking water samples from three different surface water treatment plants supplying water to the city of Paris (France). METHODS AND RESULTS: A molecular analysis was performed on a sample from each site based on sequencing of PCR amplified and cloned 18S ribosomal RNA genes. Overall, the 18S rDNA sequences combined from all samples could be affiliated to the Amoebozoa (20.8% of the phylotypes), Ciliophora (25%), Metazoa (33.3%), Fungi (8.3%), Cercozoa (4.2%) and unclassified eukaryotes (8.3%) groups. CONCLUSIONS: The 18S rDNA sequences affiliated to the Amoebozoa, Ciliophora and Metazoa lineages were found to be the most abundant phylotypes observed in the drinking water samples. Phylotypes found to be present in two, or all three, samples (41.7% of the total) may represent groups with members adapted to drinking water treatment plant (DWTP) ecosystem conditions. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that finished drinking water can contain 18S rDNA sequences representing a variety of eukaryotic taxa. Further research is needed to better characterize the eukaryotic biodiversity of DWTPs and the effects of the finished drinking water diversity on the downstream water distribution network.