Klebsiella pneumoniae is associated with substantial economic losses in the fish industry and with food-borne illness in humans. This study aimed to determine the incidence and antibiogram profiles of multi-drug resistant Klebsiella pneumoniae strains isolated from diseased Clarias gariepinus. A total of 384 diseased Clarias gariepinus that showed clinical signs of red spots and hemorrhages on the pectoral fin were sampled from commercial fish farms in Lagos, Ogun, and Oyo States, Nigeria. Samples of fin, liver, kidney, and gill were taken from diseased C. gariepinus. Samples were subjected to bacteriological examinations and isolates were identified based on morphological characteristics, biochemical tests, and 16 S rRNA gene characterisation. The retrieved isolates were tested for sequence analysis and antibiogram profile. The incidence of K. pneumoniae among the examined diseased Clarias gariepinus was 61.7% (237/384). The highest prevalence was observed in the gill (32.9%). The percentage of K. Pneumoniae isolates in diseased C. gariepinus from selected Southwest states were; Lagos State 46.8%, Ogun State 78.1%, and Oyo State 60.1% (p > 0.05). The phylogenetic analyses revealed that the tested K. pneumoniae strains shared high genetic similarity with other K. pneumoniae strains from South Africa, Saudi Arabia, India, USA, Spain, Bangladesh, and China. Antibiogram profiles revealed that 100% (120/120) of the retrieved K. pneumoniae strains were MDR to four different antimicrobial classes (penicillins, tetracyclines, nitroimidazole, and macrolides). This is the first report to reveal the occurrence of MDR K. pneumoniae in diseased C. gariepinus, an emergence that represents a risk to public health.