This is a case study of the incidence of diphtheria in National Ear Care Centre Kaduna. Samples included all patients presented with diphtheria symptoms referred to the hospital from October to December; 2018. A total of 8 patients were referred and several samples taken for laboratory investigations. 8 throat swabs were collected for organism isolation by inoculation on some certain agars, incubation, secondary gram and microscopy; colonies appeared to be biconcave, large and whitish. Microscopy revealed characteristic Chinese lettered, pleomorphic bacillus which are features of Corynebacterium diphtheriae. Blood samples were used for urea and creatinine estimation which yielded abnormal high values in all except the creatinine of one of the samples indicating kidney impairment which could be attributed to presence of the tox gene. To further confirm the incidence of the disease; one throat swab was saved at 4°C for molecular confirmation and characterisation of the gene. It was then transported to Molecular laboratory and the DNA extracted using the phenol/chloroform extraction method. Both the A and B subunits of the tox gene were amplified from the DNA extract at 248bp and 297bp respectively. Sanger’s Dye Terminator Cycle Sequencing (DTCS) of both the subunits of the tox gene was carried out and the sequences were obtained and converted to the fasta format using a Finch TV for bioinformatics analyses using the NCBI blast tool. The A and B subunits showed a percentage identity of 99.59% and 95.57% to Corynebacterium diphtheriae mitis strain NCTC 3529 genome assembly, chromosome: 1 respectively. The A subunit also showed 99.59% identity to Corynebacterium diphtheriae strain BQ11 chromosome; complete genome while the B subunit also showed 95.57% identity to Corynebacterium diphtheriae mitis strain NCTC 7838 genome assembly chromosome: 1. A mutation was also discovered in the tox genes as indicated by the E-value of 3e-84 and 2e-121 for A and B subunits respectively which are values that are less than 1. This is also confirmed by 5 gaps noticed from the blast results (4 gaps from A and 1 from B) indicating the presence of indels. In conclusion; there are confirmed incidences and sporadic cases of diphtheria in Kaduna State and the organism is said to have mutated.