A flow cell set-up was used as a model drinking water distribution system to analyze the in situ microbial population. Biofilm growth was followed by transmission light microscopy for 81 days and showed a biofilm consisting of microcolonies separated by a monolayer of cells. Protozoans (ciliates and flagellates) were often seen attached to the microcolonies. The biofilm was hybridized with oligonucleotide probes specific for all bacteria and the α- and β-subclass of Proteobacteria and visualized with a scanning confocal laser microscope. Hybridization showed that the microcolonies primarily consisted of a mixed population of α- and β-Proteobacteria. 65 strains from the inlet water and 20 from the biofilm were isolated on R2A agar plates and sorted into groups with amplified rDNA restriction analysis. The 16S rDNA gene was sequenced for representatives of the abundant groups. A phylogenetic analysis revealed that the majority of the isolated strains from the bulk water and biofilm were affiliated to the family of Comamonadaceae in the β-lineage of Proteobacteria. The majority of the strains from the α-lineage were affiliated to the family of Sphingomonadaceae. We were unable to detect any strains from the Pseudomonas genus and found a low abundance of bacteria affiliated to the γ-subclass of Proteobacteria where Pseudomonas and E. coli are positioned. The analysis revealed a high bacterial diversity in the water phase as well as the biofilm, but no strains were found in both environments.