Objectives: To identify microorganisms isolated from patients wearing different types of fixed orthodontic appliances and evaluate the resistance of isolated bacterial strains to different antimicrobials. Materials and Methods: Nineteen patients indicated to undergo fixed orthodontic treatment were chosen for the study and were divided into 3 groups -7 patients in group 1 ( conventional metal brackets), 6 patients in group 2 (conventional ceramic brackets), and 6 patients in group 3 (Passive self-ligating metal system). Plaque biofilm formed around orthodontic brackets was collected, samples were plated onto brain heart infusion agar and mitis salivarius agar and were incubated. Similarly, samples were collected in blood broth and were streaked onto blood agar to evaluate the anaerobic colony counts. Results: Maximum aerobic and anaerobic bacterial count was seen in group 2 and least in group 3. Most prevalent microbial genera were streptococcus mutans showing predominantly sensitive strains with one strain from Group 3 which showed resistance against amikacin, cefazolin, cefixime, and cefazolin. Conclusions: The number of aerobic and anaerobic CFU/ml is higher on the surface of ceramic brackets when compared to the conventional metal or the Passive self-ligating system. Streptococcus mutans was most prevalent bacterial strain amongst all aerobic bacteria isolated from all three groups.