The presence of distinct bacterial species is found to be dependent on age, diet, and disease. We compared the detection rate of several oral bacterial strains in a cohort of 36 subjects including healthy volunteers, periodontal patients, and oral cancer patients. Gargling samples were obtained from these subjects from which DNA was then extracted. Specific primers for 29 bacterial species were used for PCR detection. In the oral cancer patients, Capnocytophaga ochracea, Gemella morbillorum, and Streptococcus salivarius were detected more frequently compared with the healthy volunteers and periodontitis patients. Fusobacterium nucleatum/ polymorphym and Prevotella nigrescens were significantly less prevalent in oral cancer patients than the other groups. In periodontitis patients, Porphyromonas gingivalis and Treponema denticola were more frequently found compared with the healthy volunteers. In the healthy volunteer group, Peptostreptococcus anaerobius was more frequently found than the other groups. The detection rate of several oral bacterial species was thus found to differ between healthy volunteers, periodontitis patients and oral cancer patients.