The objective of the present investigation is to compare the effect of topical application of Doxycycline 10% (Atridox TM ) following scaling and root planning, thus, versus scaling and root planning alone on the sub- gingival plaque composition of patients with generalized severe chronic pe- riodontitis. Using split mouth design, subgingival plaque samples were taken at the baseline and 2 months after treatment. Microbiological analysis was carried out using checkerboard DNA probe technology. Plaque samples were screened for the presence of Actinomyces naeslundii, Tannerella for- sythia, Campylobacter conscisus, Campylobacter curva, Campylobacter rectus, Capnocytophaga sputigena, Eikenella corrodens, Fusobacterium nu- cleatum ss vincentii, Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens, Streptococcus oralis, Treponema denticola, and Ag- gregatibacter actinomycetemcomitans serotype b. After two months post- treatment, there was a significant decrease in total bacterial counts in both groups. Pathogens such as Tannerella forsythia, Porphyromonas gingivalis and Treponema denticola were reduced significantly when Atridox TM was used in addition to scaling and root planning, while Actinomyces naeslundii and Streptococcus oralis levels were increased. The topical application of Doxycycline 10% as an adjunct to scaling and root planning is beneficial to the non-surgical management of patients with generalized severe chronic pe- riodontitis.