Objective: The detection of special bacterial species in patients with periodontitis is considered useful for clinical diagnosis and treatment. The aim of this study was to investigate the presence of specific periopathogens and investigate whether there is a correlation between the results of different bacterial species in whole saliva and pooled subgingival plaque samples (healthy and diseased sites) from individuals with periodontitis and periodontally healthy subjects. Materials and methods: In total, 52 patients were recruited and divided into two groups: non-periodontitis and periodontitis patients. For each group, the following periodontal pathogens were detected using real-time polymerase chain reaction: A. actinomycetemcomitans JP2 clone, A. actinomycetemcomitans non JP2 clone, Porphyromonasgingivalis, and total eubacteria. Results: Higher levels of the various studied bacteria were present in both saliva and plaque samples from the periodontitis group in comparison to non-periodontitis subjects. There were significant differences in P. gingivalis and A. actinomycetemcomitans JP2 clones in the saliva of periodontitis patient compared to the control group. Subgingival plaque of diseased sites presented a significant and strong positive correlation between A. actinomycetemcomitans and P. gingivalis. In saliva samples, there was a significant positive correlation between A. actinomycetemcomitans JP2 clone and P. gingivalis (p ≤ 0.002). Conclusion: Quantifying and differentiating these periodontal species from subgingival plaque and saliva samples showed a good potential as diagnostic markers for periodontal disease. Regarding the prevalence of the studied bacteria, specifically A. actinomycetemcomitans JP2 clone, found in this work, and the high rate of susceptibility to periodontal species in Africa, future larger studies are recommended.