OBJECTIVE To evaluate the changes in the clinical parameters, and the prevalence and quantities of three major periodontopathic bacteria, namely Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans, and Tannerella forsythia, in subgingival plaque collected from patients with generalized chronic periodontitis (GCP) or generalized aggressive periodontitis (GAgP) in response to nonsurgical periodontal therapy. METHODS 73 GCP patients and 57 GAgP patients were enrolled in this study. Clinical parameters, including probing depth (PD), clinical attachment loss (CAL), and Sulcus Bleeding Index (SBI) were measured. The prevalence and quantities of the three bacteria collected from the subgingival plaque were detected by real-time PCR. Both clinical and microbiologic parameters were evaluated at baseline, 4, and 12 weeks after the nonsurgical periodontal treatment. RESULTS PD, CAL, and SBI were significantly improved in GCP and GAgP groups at 4 and 12 weeks after nonsurgical periodontal therapy, compared to the baseline levels. The prevalence and quantities of P gingivalis in GCP at baseline (82.19% and 3.35E+5) were statistically higher than those found in GAgP (66.67% and 1.08E+5; P < .05). After therapy, the prevalence and quantities of the three bacteria were sufficiently reduced in both groups at 4 and 12 weeks. There was no significant difference in improvement of clinical and microbiologic parameters between the GCP and GAgP patients after treatment. CONCLUSIONS There was a difference in P gingivalis prevalence and quantity between the GCP and GAgP patients at baseline. In addition, nonsurgical periodontal therapy was effective in the treatment of clinical symptoms and the major periodontopathic bacterial control between GCP and GAgP patients.