Purpose: The aim of this study was to evaluate the formed biofilm on two types of implant surfaces (hydrophilic or hydrophobic) associated with titanium (Ti) or zirconia (Zn) abutments. Materials and Methods: Samples were separated into four groups according to type of surface and abutment used (n = 10): (1) hydrophobic/Ti abutment, (2) hydrophilic/Ti abutment, (3) hydrophobic/Zn abutment, and (4) hydrophilic/Zn abutment. Implant-abutment assemblies were incubated with human saliva and supragingival biofilm. Samples of biofilm were evaluated by DNA Checkerboard hybridization, identifying up to 41 species. Scanning electron microscopy (SEM) images were obtained from the implants and abutments. Results: The microbial count was higher for samples from groups with the hydrophilic/Ti abutment, followed by hydrophobic/Zn abutment, hydrophilic/Ti abutment, and hydrophobic/Zn abutment (P .05). Hydrophilic surfaces and Zn abutments showed the highest counts of microorganisms. Individual bacterial counts were variable between groups; the hydrophilic/Zn abutment group had the highest microbial diversity, including T forsythia, P nigrescens, S oralis, S sanguinis, L casei, M orale, P aeruginosa, P endodontalis, S aureus, S gallolyticus, S mutans, S parasanguinis, S pneumoniae, and C albicans. The hydrophilic/Ti abutment group had the highest count of T forsythia and T denticola, microorganisms of Socransky red complex. The SEM images showed the bacterial colonization in both surfaces of the implant and abutment. Conclusion: Different surfaces of implants and abutments showed significant differences in the count and diversity of species. The hydrophilic/Zn abutment group presented the highest count and diversity of target species. Keywords: abutments, biofilms, dental implant, microbiology, prosthetic, surfaces, titanium, zirconia