Periodontal diseases include a wide range of pathological conditions, damaging the supporting structures of the teeth. Origin and propagation of periodontal disease is believed to be caused by dysbiosis of the commensal oral microbiota. The aim of this study was to evaluate the presence of bacteria in the pulp cavity of teeth with severe periodontal disease with clinically intact external surface. Periodontal (P) and endodontic (E) tissue samples of root canals from six intact teeth of three patients were sampled for analysis of microbial population using Nanopore technology. Streptococcus was the predominant genus in E samples. Porphyromonas (33.4%, p = 0.047), Tannerella (41.7%, p = 0.042), and Treponema (50.0%, p = 0.0064) were significantly more present in P than in E samples. Some samples (E6 and E1) exhibited a remarkable difference in terms of microbial composition, whilst Streptococcus was a common signature in samples E2 to E5, all which were obtained from the same patient. In conclusion, bacteria were identified on both the root surface and the root canal system, thus demonstrating the possibility of bacteria to spread directly from the periodontal pocket to the root canal system even in the absence of crown's loss of integrity.