Many utilities that have implemented chloramination for secondary disinfection experience problems with the growth of nitrifying bacteria in the distribution system. This study involved the application of molecular biology techniques to explore the types of ammonia-oxidizing bacteria (AOB) and nitrite-oxidizing bacteria (NOB) growing in three full-scale chloraminated systems showing chemical evidence of a nitrification episode. The results indicated a general dominance of the AOB populations by Nitrosomonas species, with Nitrosospira constituting a negligible or small fraction of the AOB community in all but one sample. Cloning and sequencing demonstrated the presence of Nitrosomonas oligotropha cluster representatives. For the NOB communities, Nitrospira were detected in most of the samples, while Nitrobacter were only detected in a few samples. These results provide insight into the types of AOB responsible for nitrification episodes in chloraminated systems, which should help direct future studies aimed at characterizing relevant AOB growth and inactivation properties. Also, the detection of NOB in most of the samples suggests a need to evaluate the contribution of biological nitrite oxidation relative to chemical oxidation by chloramine residual in these systems. Includes 37 references, tables, figures.