Odontogenic cysts are slow growing lesions which are formed by epithelium. They may reach to a substantial size without symptoms for a long time. Radicular cysts' (RCs) and odontogenic keratocysts' (OKCs) are common odontogenic cysts of jaws. The main purpose of this study is to evaluate if anaerobic bacteria play a role in the pathogenesis of the RCs and OKCs fluids by polymerase chain reaction (PCR). Odontogenic cyst fluid samples with a history of infection were collected from a total of 28 odontogenic cysts consisting of 16 samples of OKCs and 12 samples of RCs. Anaerobic bacteria detection were performed by PCR based on bacterial 16S rRNA genes. Porphyromonas gingivalis existed more frequently compared to the other bacteria, in all samples (39.2%). Following this, F. nucleatum (32.1%), Provetella intermedia and Campylobacter rectus (25.5%), Treponema denticola (25%), Provetella nigrescens and Tannerella forsythia (17.8%), Dialister pneumosintes (14.2%), Filifactor alocis (10.7%), Porphyromonas endodontalis and Provetella pallens (7.1%) were seen. The 58.3% of the Fusobacterium nucleatum positive cyst fluids were in the RCs group. In D. pneumosintes positive cysts liquid samples, C. rectus was found to be positive (p=0.025). The same correlation was observed between F. alocis and C. rectus (p= 0.003). On the other hand, in F. alocis positive cysts liquid samples, F. nucleatum also was found to be positive (p=0.026). Odontogenic cysts fluid contained numerous anaerobic bacteria of various types, thus suggesting that oral bacteria may cause symptoms in odontogenic cyst fluids. Further studies are needed to assess the role of these bacteria in the pathogenesis of odontogenic cysts.