Multidrug resistance (MDR) is a global threat due to either improper diagnosis or overuse of antibiotics. Head and neck infections (HNI) are serious diseases that involve several species of microorganisms. Common complications of HNI developing through bacterial colonization that leads to airway obstruction, pus collection, and sepsis. During this study, we collected 264 clinical samples (2020–2022) from Odisha, a state of eastern India to investigate bacterial communities associated with HNI followed by their antibiotic susceptibility characteristics, and the evaluation of their diversity by comparing with global isolates. We found 218 positive bacterial isolates and 25 multidrug-resistant bacteria, and accomplished their molecular characterization along with phylogenetic analysis utilizing the 16S rRNA gene. Population genetic parameters revealed the haplotype diversity (Hd) and nucleotide diversity (π) ranged from0.558-0.828 and 0.03236-0.28428 respectively. This study helps to disseminate the prevalence of these neglected pathogens within this rarely focused geographical area and its transboundary potential to navigate better therapeutic approaches.