Relevance: to indentify if periodontal treatment which is presented by photoactivated disinfection (PAD) adjunctively to scaling and root planing (SRP) yield better outcomes than ozone therapy as an adjunct to SRP in periodontitis.Materials and methods: we examined 57 (mean age 49,3 ± 1,02) patients with chronic periodontitis, divided into groups, SRP + PAD, SRP + ozone therapy and SRP alone. Subgingival plaque samples were subjected to DNA extraction and real time PCR amplifcation for detection Porphyromonas gingivalis (Pg), Prevotella intermedia (Pi), Tannerella forsythensis (Tf), Treponema denticola (Td), Aggregatibacter actinomycetemcomitans (Aa). The amount of periodontopathogens and clinical parameters including plaque index, clinical attachment loss, pocket depth, bleeding on probing were measured at baseline, after 40, 90 and 180 days.Results: the results in groups of PAD+SRP and ozone therapy+SRP showed an improvement in all clinical parameters PI, BOP, PD, CAL and the quantity of Pg, Td and Tf compared to the control group during an observation period.Conclusion: the results showed additional benefts from PAD and ozone therapy as an adjunctive treatment to SRP for patients of chronic periodontitis.