The main cause of peri-implantitis and crestal bone resorption is bacterial infection. The present study aimed to comparatively assess the microbiological parameters in sulci around teeth and crowns supported by dental implants and also compare microbiological parameters around deep and shallow implant sulci. In this cross-sectional study, 34 partially edentulous patients with a total of 72 implants (22 deep vs. 50 shallow sulci) were included. Excluded were the patients with compromised systemic and periodontal health or smoking habits. All Implants (ITI) were at least 6 month in place covered by definite prostheses. Samples of gingival sulci were taken around teeth and implants with paper points and transported in Stuart Transport Medium. Samples were cultured and examined by dark field microscope to determine the microorganisms. Data were evaluated statistically in SPSS (v11.5) using chi-square test. Cocci G+, Cocci G-, Prevotella, Porphyromonas gingivalis, Bacteroid fragilis and Fusobacterium were found. The relative frequency of P. gingivalis was significantly higher in deep implant sulci compared to shallow implant sulci (p = 0.044) and natural sulci (p = 0.009). B. fragilis was also significantly more isolated from the deep implant sulci compared to shallow implant sulci (p = 0.001) and natural sulci (p = 0.064). Within the limitations of the present study, it may be concluded that peri-implantitis is more likely in deep sulci compared with shallow sulci in partial edentulousness.