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<p><b>Objective:</b> In this study hypothesing the translocation of oral bacteria from oropharynx into the middle ear cavity may be involved in the pathogenesis of otitis media with effusion (OME), we aimed to investigate the presence and similarity of <i>Fusobacterium nucleatum</i> and <i>Treponema denticola</i> in saliva, nasopharyngeal secretion and the middle ear effusion samples from the children with OME.</p><p><b>Methods:</b> Totally 20 children with OME undergoing myringotomy and ventilation tube placement were attended. Stimulated saliva samples were collected after otorhinolaryngological and oral examinations were done. The middle ear effusion and nasopharyngeal secretions were collected during the operations. The presence of <i>F. nucleatum</i> and <i>T. denticola</i> were detected using 16SrRNA-based PCR. The clonal similarities of the bacteria were detected in the samples which the same bacteria had been detected in each samples of the same child. After DNA sequencing, clonal similarity was determined by 16SrRNA gene clone library analysis. The sequences from each clone were compared with similar sequences of reference organisms by FASTA search.</p><p><b>Results:</b><i> T. denticola</i> was detected only in four (20%) saliva and in one (5%) nasopharyngeal sample. <i>F. nucleatum</i> was detected in 11 (55%) saliva, eight (40%) nasopharyngeal and six (30%) middle ear effusion samples. Sequences from <i>F.nucleatum</i> clones derived from three different anatomic sites within patients were similar in 33% of OME patients, indicating their genetic relatedness.</p><p><b>Conclusions:</b> Bacteria involved in this process most likely originate from the oropharynx since they show a close genetic relatedness with their oropharyngeal counterparts.</p>