Background: Health crisis of multi-drug resistant Klebsiella pneumoniae (K. pneumoniae) seems overwhelming. Genotyping for such an important pathogen is a demand to control aggressive Klebsiella infections. Therefore, this study was conducted to identify the different phylogenetic groups of K. pneumoniae complex and to assess their prevalence and antimicrobial resistance patterns. Methods: Seventy-six K. pneumoniae isolates were collected and identified using conventional microbiological methods. Isolates were confirmed to be K. pneumoniae by amplification of gyrA gene by PCR. The antimicrobial susceptibility testing was performed by disk diffusion method. Restriction Fragment Length Polymorphism-PCR (RFLP-PCR) was performed for the identification of the phylogenetic groups and the relationships of these phylogroups to antimicrobial susceptibility were investigated. Results: RFLP-PCR showed that 62 isolates (81.6%) were identified as KP I, 9 isolates (11.8%) as KP II and 5 isolates (6.6 %) as KP III. Among the 62 KP I isolates, 39 isolates (63%) showed MDR and 12 (19.4%) showed XDR. While among the 9 KP II isolates, 7 isolates (77.7%) showed MDR and only one (11.1%) showed XDR. Among the 5 KP III isolates, 2 isolates (40%) showed MDR, while only one isolate (20%) showed XDR. Conclusion: Reliable identification of the three K. pneumoniae phylogenetic groups can be obtained by gyrA PCR-RFLP. The level of resistance for most of the antibiotics was highest among phylogroup I, which may start future outbreaks that could be difficult to manage by the available sets of antibiotics. This ensures the value of genomic surveillance in research, clinical and public health settings.