Copyright © 2017 Sandeep Vasaikar et al. The increase in the incidence of extended-spectrum -lactamase- (ESBL-) producing Klebsiella species has become a serious problem worldwide, because of their incrimination in antibiotic resistance.Theobjective of this study is to investigate the resistance genes responsible for ESBL-producing Klebsiella species and carbapenemase-producing Klebsiella (CRE) isolated in Mthatha and to study their epidemiology. A prospective, descriptive study of 202 nonrepetitive samples frompatients was obtained fromNelson Mandela AcademicHospital.The cultured Klebsiella isolates were subjected to antimicrobial susceptibility tests and the polymerase chain reaction of blaCTX-M, blaTEM, blaSHV, blaKPC, and blaNDM genes. Overall K. pneumoniae were the majority with 169 (83.7%) species isolates, followed by K. oxytoca with 29 (14.4%), while K. ozaenae and Raoultella ornithinolytica were 2 (0.9%) each. The prevalence of ESBL production in all Klebsiella species was 117 (57.9%). ESBL-genotypic resistance is driven in Mthatha by blaSHV 121 (77.1%) followed by blaTEM 105 (66.9%) and blaCTX-M at 89 (56.7%).The most common ESBL genotype combination among the Klebsiella was blaTEM + blaSHV + blaCTX-M at 79 (50.3%).There is a steady increase in the rate of ESBL genes in the last five years.