Background: Although Immuno inflammatory relationship between periodontal diseases and diabetes mellitus is acknowledged, the difference in putative periodontal microorganisms between diabetic and non diabetic individuals is not well established. Aim: To compare the prevalence of two putative periodontal pathogens namely Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis in Type II Diabetic and Non Diabetic patients with chronic periodontitis by Polymerase chain reaction Materials and Method: Sixty subjects were selected from the Department of Periodontics, Tamilnadu Government Dental College and Hospital, Chennai __ampersandsignndash; 03. 30 Type II diabetic patients with chronic periodontitis were categorized as Group I and 30 Non diabetic patients with chronic periodontitis were categorized as Group II based on American Dental Association classification 1997 and American Academy of Periodontology classification 1999. Two sites- 1 healthy site and 1 diseased site were chosen in each patient, Group I H, II H __ampersandsignndash; healthy site samples and Group I D, II D- diseased sites samples. Subgingival plaque was collected, DNA isolation was done __ampersandsignamp; the presence of A.actinomycetemcomitans __ampersandsignamp; P.gingivalis DNA was determined by PCR. The PCR products were sequenced and confirmed. The data was statistically analysed. Results: A.actinomycetemcomitans was detected in 6.7 %, 6.7%, 13.3%, 10% in Groups I H, II H, I D, II D respectively. P.gingivalis was detected in 40%, 46.7%, 46.6%, 53.3% in Groups I H, II H, I D, II D respectively. When comparisons were made between Groups I H __ampersandsignamp; II H and Groups I D __ampersandsignamp; II D for the two organisms, no statistically significant difference was obtained Conclusion: The present study shows no statistically significant difference in the prevalence of A.actinomycetemcomitans and P.gingivalis in Type II Diabetic and Non Diabetic patients with chronic periodontitis.