Objective This study was designed to investigate the differences among six periodontal pathogens from the subgingival plaque of chronic periodontitis(CP) patients living in high-altitude and plain areas. Methods Subgingival plaque samples were collected from 20 CP patients and 20 periodontal healthy(PH) subjects living in high-altitude or plain areas. Six periodontal pathogens, which includes Porphyromonas gingivalis(P. gingivalis), Tannerella forsythia(T. forsythia), Treponema denticola(T. denticola), Actinobacillus actinomycetemcomitans(A. actinomycetemcomitans), Prevotella intermedia(P. intermedia), and Fusobacterium nucleatum(F. nucleatum), were detected by 16S rRNA polymerase chain reaction. Results P. gingivalis, T. forsythia, T. denticola, A. actinomycetemcomitans, P. intermedia, and F. nucleatum were detected more frequently in high-altitude CP patients(with corresponding prevalence rates of 90%, 100%, 80%, 60% and 85%) compared with high-altitude PH controls(P