Young adults are susceptible to chronic periodontal disease. Chronic periodontitis is thought to arise from the complex microflora in the oral cavity, which includes some putative periodontopathic bacteria. To unveil the diversity of periodontopathic bacteria, we conducted amplified ribosomal DNA restriction analysis (ARDRA) to investigate and compare the bacterial diversity in the subgingival plaque (SP), gingival crevicular fluid (GCF), and saliva samples of young adults with chronic periodontitis. Diversity indices were calculated by ARDRA results, which revealed that the bacterial communities in SP were more diverse than those in the GCF and saliva. In total, 65 operational taxonomic units from the SP library were identified and sequenced for phylogenetic analysis. These sequences could be assigned to 18 known bacterial genera, of which 15 are known to exist in the human oral cavity. The results of the phylogenetic study show that the predominant species in the SP of patients with chronic periodontitis are obligate anaerobes (Selenomonas, Leptotrichia, Lachnospiraceae, Eubacterium, and Fusobacterium species), and that Gram-negative bacteria are associated with chronic periodontitis. These findings demonstrate the diversity of bacteria that exist in chronic periodontitis, which should be considered in the treatment strategy for these patients.