Dental implant surgery has been a successful therapeutic option for the rehabilitation of partially or completely edentulous jaws for many years. However, evidence regarding the causative factors of peri-implant disease is still lacking. Peri-implantitis is an inflammatory disease affecting the soft and hard tissues surrounding osseointegrated implant associated with the formation of a bacterial biofilm on the implant surface close to the marginal tissues. The aim of this chapter is to summarize the knowledge regarding the microbiota associated with peri-implant infection and to review the different microbial diagnostic tests to understand the peri-implant microbiota, as well as summarize the present knowledge regarding management of peri-implantitis and propose further recommendations for future studies. This chapter shows that the scientific data regarding the microbiota responsible for peri-implantitis initiation and progression are still inconclusive. A microbiological test may thus be one diagnostic method to be used to understand the complexity of microbiota associated with the peri-implant sulcus. However, in order to resolve inflammation and arrest disease progression, the understanding of the biofilm development is essential.