Periodontal disease is the most common infectious disease of cats and dogs which are strongly associated with periodontal pathogens. The primary etiologic factor in the formation of periodontal disease is microbial dental plaque accumulation on teeth. In our research, we aimed to investigate the presence of periodontal disease-related bacterial species in dental plaques of cats and dogs. Specimens collected from 50 cats and 51 dogs with periodontal disease examined in terms of periodontal pathogens by polymerase chain reaction (PCR) using primers directed to 16S rRNA and tdpA genes. Our findings indicate the presence of periodontal disease-related pathogens, especially Porphyromonas gingivalis (cats 96%, dogs 88%), Prevotella nigrescens (cats 90%, dogs 57%) and, Porphyromonas gulae (cats 70%, dogs 39%). In addition, the prevalence of Tannerella forthysia (cats 2%, dogs 4%) well-known pathogen in cats and dogs were isolated with an extremely low percentage.