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Research has focussed on the identification of novel hidden pathogens that might contribute to the pathogenesis of periodontal disease. Chronic periodontitis appears to have a complex bacterial etiology. Inspite of advanced therapeutic modalities aimed at complete elimination of periodontal pathogens, the prevalence of periodontal diseases is increasing. The advent of molecular methods like PCR, hybridization techniques and DNA probes has made the identification of uncultivated species achievable. The novel pathogens enlisted under periodontal phylogeny include Cryptobacterium curtum, Dialister pneumosintes, Filifactor alocis, Mitsuokella dentalis, Slackia exigua, Selenomonas sputigena, Solobacterium moorei, Treponema lecithinolyticum, Synergistes. These newly identified pathogens were classified based on the significant association with periodontitis into higher, moderate levels, lower levels of association.