Periodontal disease is a complex inflammation/immune-mediated compromising of connective and epithelial tissues in dental periodontal ligament. Serving as a stabilizing and mechanical absorption system, periodontal ligament consist in a complex and organized structure presenting a really delicate balance with oral microbioma and immunomediated alterations. A large number of microbiological assays have been developed to understand, prevent and even stabilize an advanced disease form. Specific protozoic organism, usually not triggered in conventional microbiological assays, could not be evaluated and underestimated by the clinician. Their role, pathogenetic mechanism and agonist activity is far to be completely known. As a matter of fact, protozoic organism is still possibly involved in determination of chronical periodontitis and their knowledge is essential for a comprehensive overview in microbioma-mediated oral and gingival alteration. E. gingivalis and T. tenax are strongly associated with non responsive chronic periodontal disease. These pathogen organisms must be clearly and carefully identified and evaluated for a possible antagonistic spontaneous conversion. These conditions could be largely observed in unbalanced oral microbiome and patient with poor oral hygiene. Understanding prevalence, epidemiological aspects, pathological mechanism, therapies and role of hygiene therapy must be a fundamental knowledge of modern dental clinicians.