A comparison of the quantification of a specific microbial group in activated sludge by fluorescent in‐situ hybridization, coupled with either direct microscopic counting or flow cytometry, was performed using an enhanced‐biological‐phosphorus‐removal, sequencing‐batch reactor. The population dynamics of Candidatus Accumulibacter phosphatis (Cand. A. phosphatis) was evaluated during two separate runs of the reactor. With the operational conditions used, Cand. A. phosphatis was enriched until a failure in the pH controller eliminated its ecological advantage. As a result, the comparison of quantification techniques included Cand. A. phosphatis concentrations as low as 11% and as high as 96% of the total cells in the samples. The analysis demonstrated that, regardless of the particular limitations of each technique, both provided similar results when the activated‐sludge flocs were easily dispersed. However, when the activated‐sludge samples contained flocs that were difficult to disperse, flow cytometry failed to provide quantitative results.