The oropharyngeal area can be a source of halitosis. However, the relationship between healthy tonsillar microbiota and halitosis is poorly understood. We conducted a pilot clinical study to clarify the effect of gargling with an antiseptic agent on tonsillar microbiota in patients with halitosis. Twenty-nine halitosis patients who did not have otolaryngologic disease or periodontitis were assigned randomly to one of three groups: benzethonium chloride (BZC) gargle; placebo gargle; no gargle. Concentrations of volatile sulfur compounds (VSCs) in mouth air, the organoleptic score (ORS) and tongue-coating score (TCS) were measured before and after testing. Tonsillar microbiota were assessed by detection of periodontal pathogens, and profiling with terminal restriction fragment length polymorphism (T-RFLP) analysis and sequencing of 16SrRNA clone libraries for taxonomic assignment. Gargling with BZC reduced the concentrations of methyl mercaptan and hydrogen sulfide and the ORS, but did not affect the TCS or prevalence of periodontal pathogens. T-RFLP analyses and 16SrRNA clone sequencing showed a tendency for some candidate species to decrease in the test group. Although gargling of the oropharyngeal area with an antiseptic agent can reduce oral malodor, it appears that tonsillar microbiota are not influenced greatly.