Dental caries is a chronic infectious disease of teeth with a polymicrobial etiology. Periodontitis is a common oral inflammatory disease of periodontal tissue caused by complex bacteria. The aim of this study is to find out whether caries-active, periodontitis and orally healthy controls were associated with a unique bacterial profile separately, and to figure out the relationship and bacterial biomarkers of dental caries and periodontal disease. The unstimulated saliva samples were collected from 124 individuals (including 38 patients with caries-active, 34 patients with periodontitis, 15 patients with both caries-active and periodontitis, and 37 orally healthy controls). The Illumina Hiseq sequencing was employed by the amplification of 16S rDNA V3-V4 hypervariable regions to analyze salivary bacterial profiles.