Cell phenotype is influenced by the linear sequence of bases and by epigenetic changes. Despite the huge number of implants placed every year, epigenetic mechanisms controlling peri-implant processes remain unexplored. The purpose of this systematic qualitative review was to investigate the available articles dealing with the relationships between DNA methylations, histone modifications, or micro-RNA (miRNA) production and implant therapy. A large variety of different surfaces were evaluated based on their osteogenic stimulation of osteoblasts. Dental implant treatments like potassium hydroxide (KOH) alkali-etching, electrolytic etching, ionization, functionalization with miRNAs or anti-miRNAs, or osteogenic peptides enhanced osteoblast differentiation and gene activation by regulating miRNA production. Zirconia and anatase coating inhibited the activation of osteogenic genes. Epigenetic changes on peri-implant cells induced by smoking still remain unclear. Due to the heterogeneity of methodologies, a meta-analysis was not possible. Even if it is impossible to define which implant surface was best to genetically stimulate osteogenesis, there is evidence that implant surface features can upregulate or downregulate genes related to osseointegration.