The purpose of this study is to compare the effectiveness of muco-adhesive Nigella Sativa extract with muco-adhesive Thymoquinone as an adjunctive topical treatment medicine following scaling and root planning (SRP), and to compare them with the outcomes of treating chronic periodontitis by performing SRP only. This is a randomized, triple-blind, placebo controlled study. Samples are chosen from patients suffering from chronic periodontitis who referred to Kermanshah Faculty of Dentistry. Inclusion criteria: patient free from systemic illness; patient who had not taken periodontal therapy in the past 3 month Exlusion criteria: dissatisfaction and inability to comply with the follow-up visit requirments; history of systemic illness; received antioxidants like vitamin C and E or β-Carotene; pregnant. In each patient after scaling and root planing, muco-adhesive Nigella Sativa gel is injected in one site, muco-adhesive Thymoquinone gel is injected in another site and on the third site placebo is injected. Clinical parameters to be considered including plaque index, gingival index, pocket depth, clinical attachment loss, and bleeding index are evaluated pre-treatment and in 8, 15, 30, and 90 days post-treatment.