Objective: To investigate the changes of the bacterial community in the oral environment of beagle dogs to gain insights on the possible causes of failed therapy in peri-implantitis. Methods: Beagles were used as models for experimental peri-implantitis. Samples from peri-implant soft tissue (supramargin and submargin), ligature and contaminated surface of peri-implantitis sites were collected and analysed by sequencing the bacterial 16S rRNA gene. Results: The residual microbial community from the curettes-treated implant surface contained a variety of microorganisms, including periodontal pathogens, which showed no changes in their composition and structure. Conclusion: It is possible that the residual bacterial community remained unchanged and this was the cause of recurrent episodes of inflammation. Keywords: peri-implantitis, microbial communities, peri-implant mucositis, peri-implant soft tissue, biofilm