In this study, we analyzed changes in the community structure of sulfur-oxidizing bacteria (SOB) in a wastewater treatment process handling urban sewage over a 1-year period. Facultative anaerobic SOB, which can use nitrate as an electron acceptor, were predominant over obligate aerobic SOB in the activated sludge tank and clarifier/settler throughout the investigation period, with mixotrophic SOB being the dominant group. Facultative anaerobic SOB were predominant in most wastewater treatment facilities included in our comparative analysis, confirming observations in the investigated facility. Although the constituent species of SOB in the activated sludge tank and clarifier/settler remained consistent over the investigation period, the proportion of SOB relative to all analyzed sequences fluctuated between 0.91% and 6.20%, with periodic increases and decreases. Sulfuritalea hydrogenivorans, which was the predominant SOB in the activated sludge tank at the investigated facility, exhibited maximum and minimum 11.1- and 6.8-fold differences in abundance between the open and closed tanks, respectively. We conclude that sulfur oxidation by SOB during wastewater treatment can contribute to denitrification under anaerobic conditions. Furthermore, the population of predominant SOB species in the investigated wastewater treatment facility exhibited cyclical fluctuation.