The inflammatory periodontal disease pathogenesis is determined by microorganisms of the oral cavity. Along with the well-studied periodontopathogens, microbial agents of unproven clinical significance, including epibiotic bacteria, are found in individuals with gingivitis and periodontitis. The study aimed to determine the association between the Nanosynbacter lyticus epibiont and inflammatory periodontal diseases. Conservative DNA sequences specific for the genera Nanosynbacter, Schaalia and the Bacteria domain were identified using PCR in 47 study participants (31 females and 16 males) aged 18–45 years. The results were expressed as indices determining the quantitative relationships between N. lyticus and Schaalia spp. (NS index), as well as between N. lyticus and representatives of the Bacteria domain (NB index). Schaalia spp. were not found in a large share (11/27, 40.7%) of patients with no periodontitis. All patients with moderate-to-severe periodontitis, as well as 75% of patients with mild periodontitis were carriers of Schaalia spp. All the Schaalia-positive samples from patients with periodontitis showed higher NS indices (p < 0.05) compared to Schaalia-positive samples from patients with no periodontitis: the median NS values were Ме = 0.89 (0.79; 0.93) and Ме = 0.63 (0.00; 0.73), respectively. The patients suffering from chronic generalized periodontitis had significantly higher NB indices (Ме = 0.83 (0.79; 0.85)) (p < 0.05) compared to patients with no periodontitis, Ме = 0.67 (0.00; 0.81).