Osseointegrated dental implants are now a well-established treatment option in the armament of restorative dentistry. These technologically advanced devices are designed to functionally and esthetically replace missing teeth. Despite the revolutionary advances that implants have incurred, they have also provided the oral cavity with new artificial surfaces prone to the formation of oral biofilms, similarly to the hard tissue surfaces of natural teeth. Biofilm formation on the implant surface can trigger the inflammatory destruction of the peri-implant tissue, in what is known as peri-implantitis. The mixed microbial flora of peri-implant infections resembles that of periodontal infections, with some notable differences. These are likely to expand with the ever increasing application of metagenomics and metatrascriptomics in the analysis of oral ecology. This review presents the wealth of knowledge we have gained from microbiological methods used in the characterization of peri-implant microflora and sheds light over potential new benefits, as well as limitations, of the new sequencing technology in our understanding of peri-implant disease pathogenesis.