Purpose: The purpose of this study was to compare zirconium oxide and titanium alloys with respect to their tendency to adhesion and colonization of two periodontal pathogens on both hard surfaces and on soft tissues in vivo. Materials and Methods: The present study was designed as a prospective stratified randomized controlled clinical trial. Patients were scheduled to receive two implants with different types of abutments in the posterior mandible. Three months after implant placement, titanium and zirconium abutments were connected. Five weeks after abutment connections, the abutments were removed, probing depth measurements were recorded, and gingival biopsy samples were obtained. Abutments and biopsy specimens were analyzed by reverse-transcriptase polymerase chain reaction to compare the DNA copy numbers of Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, and total bacteria. The surface free energy of the abutments was calculated by sesile water drop before replacement. Results: No statistically significant differences were found between probing depths or DNA copy numbers of A actinomycetemcomitans, P gingivalis, and total bacteria both for both titanium alloys and zirconium oxide surfaces and the biops specimens obtained from their buccal gingival. With respect to the surface free energy of zirconium and titanium abutments, zirconium abutments showed lower surface free energy than titanium abutments. Conclusion: The results of this study showed that zirconium oxide surfaces have comparable properties to titanium alloy surfaces in their tendency to adhesion and colonization of two periodontal pathogens on both hard surfaces and in soft tissues. Keywords: dental implants, real-time polymerase chain reaction, titanium alloys, zirconium oxide