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Introduction: Diphtheria caused by toxigenic Corynebacterium diphtheriae is an acute respiratory infection characterised by pseudomembrane formation in the throat. Although diphtheria is often reported sporadically across India, molecular characterisation of C.diphtheriae strains could play a crucial role in epidemiological investigations. Aim: To perform molecular characterisation of Corynebacterium diphtheriae isolates of faucial diphtheria cases from Assam, North-East India utilising Multi-Locus Sequence Typing (MLST). Materials and Methods: In this cross-sectional study, three isolates were obtained from three different cluster of cases that occurred across two districts of Assam, India for a period from November 2019 to June 2020. The MLST of these three C.diphtheriae isolates were performed in Multidisciplinary Research Unit of Assam Medical College and Hospital by using the 7-gene MLST alleles of C.diphtheriae to determine the Sequence Types (ST). Results: The MLST of the three isolates of this study revealed two distinct STs, ST-588 and ST-576 with multi-clonal lineages with ST-466, reported in C.diphtheriae strains of North Kerala and ST-301 related strains of Bangladesh, respectively. Conclusion: In spite of frequent reports of diphtheria cases from Assam, molecular typing of the C.diphtheriae strains found in North-Eastern region of India has not yet been performed. This is one of the initial investigations from this region of India to use MLST for typing C.diphtheriae strains. Therefore, studies related to molecular characterisation of C.diphtheriae strains found throughout India could immensely help in determining the clonality and diversity existing among these strains. [ABSTRACT FROM AUTHOR]