The closely related species Actinobacillus actinomycetemcomitans, Hemophilus aphrophilus and Hemophilus paraphrophilus are common findings in oral microbiota. The aims of this study were to compare the distribution of three species in healthy subjects and periodontitis patients using PCR for 16s rRNA gene. The DNA was extracted from the subgingival plaque and saliva in 122 subjects for restriction enzyme analysis with Hinf I and Hha I. In case of periodontally healthy person, A. actinomycetemcomitans was predominant than H. paraphrophilus in saliva sample, but H. paraphrophilus was predominant than A. actinomycetemcomitans in subgingival plaque sample. On the contrary, in case of periodontitis patients, H. paraphrophilus was predominant than A. actinomycetemcomitans in saliva sample, but A. actinomycetemcomitans was predominant than H. paraphrophilus in subgingival plaque sample. In addition, the fact was confirmed that the distribution of A. actinomycetemcomitns of women periodontitis patients was somewhat higher than men periodontitis patients in saliva and subgingival plaque samples. We convinced that the PCR method for 16s rRNA gene was important for screening and monitoring of periodontal disease.