Introduction:Porphyromonas gingivalis is one among the major etiological agent in periodontal diseases and has been proved to cause gingival inflammation under orthodontic appliances.Aim:To assess the effect of amine fluoride and probiotic mouthwashes on levels of P. gingivalis during orthodontic treatment, using real time-polymerase chain reaction (RT-PCR).Materials and Methods:A randomised controlled trial was performed including 45 patients. There were three groups: Group A (control group), Group B (patients using Amflor mouthwash) and Group C (patients using probiotic mouthwash). During the treatment, all the 3 groups were advised to brush twice a day using Colgate tooth paste and Group B patients were advised to swish 15 ml fluoridated mouthwash (Amflor) and Group C advised to swish probiotic for 60 s before swallowing, once in the morning and once before sleep. After gently removing supragingival plaque, subgingival plaque samples were collected by inserting a sterile dental curette into the bottom of the gingival crevice around 31, 32, 41, and 42 at two different intervals: T1 at start and T2 after 6 months of fixed orthodontic treatment. Sub-gingival plaque samples collected were transferred to laboratory within 48 h for RT-PCR analysis in Tris-buffer solution, to maintain the integrity of bacterial DNA.Results:The levels of P. gingivalis were significantly decreased with probiotic mouth wash.Conclusions:Probiotic mouth wash can be used as an adjunctive measure along with regular brushing to improve periodontal status during fixed orthodontic treatment.