This study employed culture-independent molecular techniques to extend the characterization of the microbial diversity of biofilm associated with either titanium or zirconia implant-abutments, including not-yet-cultivated bacteria species, and to identify and quantify species recovered from peri-implantar/periodontal sulci, supragingival biofilm and the internal parts of implants. Probing depth, clinical attachment level, bleeding on probing, and marginal bone level were also evaluated over time and correlated with biofilm formation.Twenty healthy participants were analyzed. DNA-Checkerboard and 16S-rDNA-Pyrosequencing were used to quantify and determine species identity.161 bacterial taxa representing 12 different phylotypes were found, of which 25% were non-cultivable. Species common to all sites belonged to genera Fusobacterium, Prevotella, Actinomyces, Porphyromonas, Veillonella and Streptococcus. While some species were subject-specific and detected in most sites, other species were site-specific. Moderate to higher levels of unclassified species were found colonizing titanium-related sites. Pathogenic and non-pathogenic species were detected colonizing oral sites in both materials. Titanium-related sites presented the highest total microbial count and higher counts of pathogenic species.Our results revealed differences regarding microbial diversity and microorganisms counts in oral biofilm associated with titanium or zirconia. The obtained data suggests a possible relation between microbiological findings and clinical outcomes.Next-generation methods of detection have provided new insights on complex microbiota colonizing different sites of oral cavity. The present study demonstrates relevant differences in the communities and microbial counts colonizing different tested substrates with consequent significant differences in the clinical-outcomes, suggesting a probably different mechanism for specific bacterial adhesion.