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<0.05). P. gingivalis, T. forsythia, T. denticola, P. intermedia, and F. nucleatum were detected more frequently in plain CP patients(with corresponding prevalence rates of 80%, 85%, 70%, 75% and 50%) than plain PH controls(P<0.05). The detection rates of F. nucleatum and A. actinomycetemcomitans in the highaltitude CP group were significantly higher than those in the plain CP group(P<0.05). Conclusion The high-altitude CP group showed the highest detection rates for the six periodontal pathogens than the other groups. Significant differences were found in the prevalence of F. nucleatum and A. actinomycetemcomitans between the high-altitude and plain CP groups.