Exploring variations in the oral microbiome that predict the early stages of oral diseases could lead to more accurate diagnosis and therapy before the disease manifests clinically. This study compared the bacterial profile around prosthesis on natural teeth and implants in a healthy oral cavity. Fifteen participants with prosthesis on natural teeth and 15 participants with implants were recruited. All participants were periodontally healthy. Plaque samples were collected and then subjected to PCR amplification with 16S rRNA gene sequencing. Using the BlastN program, the sequenced data were compared to reference bacterial gene sequences in the Human Oral Microbiome Database. Finally, bacterial species in both groups' samples were identified, and a phylogenetic tree was created to compare the bacterial profile around prosthesis on natural teeth and implants. Microorganisms identified were <i>Streptococcus, Fusobacterium, Corynebacterium, Micrococcus, Aeromonas, Leptotrichia,</i> and <i>Dechloromonas </i>species; around implants were <i>Streptococcus, Fusobacterium, Corynebacterium, Prevotella, Eikenella, Nisseria, Rothia, Aeromonas, Leptotrichia,</i> and <i>Actinomyces</i> species. On comparing the bacterial profile around prosthesis on natural teeth and implants in periodontally healthy individuals, pathogenic bacterial species including <i>Fusobacterium nucleatum, Prevotella intermedia</i>, and <i>Eikenella corrodens</i> were identified around implants.