This cross-sectional study was carried out to identify A. actinomycetemcomitans and P. intermedia in the subgingival plaque of three ethnic groups (Malays, Chinese and Indians) in a selected group of adult Malaysians with advanced Chronic Periodontitis and to correlate these findings with their periodontal status. Thirty periodontally diseased adults were age, gender and ethnically matched with 30 healthy individuals. Clinical parameters were assessed for all. Subgingival plaque samples were collected for identification of A. actinomycetemcomitans and P. intermedia using polymerase chain reaction. Prevalence for P. intermedia (83.3%) was high and A. actinomycetemcomitans (6.7%) low in the total subject population. P. intermedia and A. actinomycetemcomitans were more prevalent in diseased (86.7%, 10% respectively) than in healthy (80%, 3.33% respectively) subjects. A. actinomycetemcomitans was detected in 15% Indians, 5% Malays but none of the Chinese subjects whereas P. intermedia was detected in 90% Malays, 85% Indians and 75% Chinese subjects. No significant association between presence of A. actinomycetemcomitans and P. intermedia with race and periodontal disease status was found. Only A. actinomycetemcomitans had a significant association with clinical attachment level (CAL) (p < 0.05). In conclusion, in this small subject group, none of the pathogens were associated with race and periodontal disease status and only A. actinomycetemcomitans had a significant association with CAL.