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Black quarter is an important bacterial disease that affects cattle and sheep with high mortality caused by Clostridium (C.) chauvoei, a Gram-positive, motile, spore producing anaerobic bacteria. The pathogen has worldwide occurrence and most blackleg cases occur in young cattle of less than two years of age, the spores are capable of existing for many years in soil. The phylogenetic positioning of C. chauvoei based on the 16s rRNA shows the pathogen close to C. septicum among the genus clostridia. The exact pathogenesis of the disease and virulence factors it harbors are so far not fully characterized. Genome sequencing is a powerful tool for understanding bacterial pathogens and their diversity. This study was envisaged to char-acterize the pathogen and understand its population diversity by whole genome sequencing. Genome se-quencing was carried out for 24 isolates of European origin. Genome assembly and annotation was con-ducted using various bioinformatics tools. The genome diversity analysis was performed after determining the maximum common genome (MCG), pairwise comparison revealed 14 to 100 single nucleotide polymor-phisms among the isolates. Genetic polymorphisms at nucleotide level were also observed among the known virulence genes for C. chauvoei such as the sialidase and flagellin genes.