The objective of this study was to monitor the impact of chlorination and chloramination treatments on heterotrophic bacteria (HB) and ammonia-oxidizing bacteria (AOB) inhabiting a water distribution system simulator. HB densities decreased while AOB densities increased when chloramine was added. AOB densities decreased below detection limits after the disinfection treatment was switched back to chlorination. The presence of AOB was confirmed using a group-specific 16S rDNA-PCR method. 16S rDNA sequence analysis showed that most bacterial isolates from feed water, discharge water, and biofilm samples were alpha-Proteobacteria or beta-Proteobacteria. The latter bacterial groups were also numerically dominant among the sequences recovered from water and biofilm 16S rDNA clone libraries. The relative frequency of each culturable bacterial group was different for each sample examined. Denaturing gradient gel electrophoresis analysis of total community 16S rDNA genes showed notable differences between the microbial community structure of biofilm samples and feed water. The results of this study suggest that disinfection treatments could influence the type of bacterial community inhabiting water distribution systems.