Purpose: To clinically assess the effects of a mouthwash containing an extract of Sambucus williamsii var. coreana, a natural ingredient, on halitosis and halitosis-causing bacteria. Materials and Methods: This randomised, double-blind, placebo-controlled study included 77 participants. The experiment was conducted at Misoplant Dental Clinic in Busan, South Korea. Participants were divided into two groups: a control group consisting of 38 participants, to who whom a saline gargle was administered 1x/day for 30 s, and an experimental group consisting of 39 participants, who used a mouthwash containing Sambucus williamsii var. coreana extract 1x/day for 30 s for 1 day or 5 days. Halitosis was measured for 30 s in the absence of brushing or moisture. A sterile #15 paper point was placed in the gingival sulcus for 10 s, after which it was analysed using the polymerase chain reaction (PCR) method. The measurement time points were defined as follows: ‘baseline’: before starting the gargling routine; ‘1 day of treatment’: immediately after gargling once on day 1; ‘5 days of treatment ’: after gargling once a day for 5 days. Clinical results were statistically analysed using SPSS 24.0 for Windows. Results: Compared to the control group, halitosis clearly decreased in the experimental groups ‘5 days of treatment’ and ‘1 day of treatment’ (p < 0.05). There were statistically significant differences in the levels of halitosis-causing bacteria between the two groups; bacterial concentration in the experimental group decreased statistically significantly from day 1 to day 5 day of gargling with Sambucus williamsii var. coreana extract (p < 0.05). Accordingly, we clinically verified that Sambucus williamsii var. coreana has antibacterial effects against oral bacteria. Conclusion: The application of Sambucus williamsii var. coreana extracts effectively reduced halitosis and halitosis-causing bacteria. Therefore, mouthwashes containing Sambucus williamsii var. coreana extract can be used as an effective substitute for chemical formulations for treating halitosis.