This study found that the ratio of Thiothrix eikelboomii to total bacterial concentrations (TH/TB) (%) was a better indicator of bulking incidents affecting effluent quality compared to absolute T. eikelboomii abundance alone. This was determined using a genus-specific Thiothrix quantitative PCR primer and probe set, which was developed in this study to monitor specific Thiothrix populations over a 1-year period. T. eikelboomii was identified as the source of bulking incidents based on sequencing of the 16S rRNA gene at a nitrifying-denitrifying wastewater treatment plant. Peak T. eikelboomii concentrations observed in March, April, and July 2009 were 2.32 x 10(10), 2.64 x 10(10), and 1.84 x 10(10) cells/l, respectively. The highest fraction of T. eikelboomii to total bacterial population was measured at 0.24% in March, and a ratio > 0.19% caused increases of suspended solids and biochemical oxygen demand in the secondary effluent. Additionally, food/mass ratios, dissolved oxygen concentrations in the anoxic selector, and ammonium ion concentrations in the primary effluent were three parameters displaying statistically significant correlations (r=0.40, r=0.50, and r=0.32, respectively) to Thiothrix spp. abundance in an aeration tank. No bulking events caused by T. eikelboomii occurred when the dissolved oxygen concentrations in the anoxic selector was maintained at lower than 0.12 mg/l and the TH/TB ratios were < 0.10%.