The study reports the complete genomic sequence of *Vibrio cholerae* El Tor N19691, a Gram-negative, γ-Proteobacterium with two circular chromosomes. The genome consists of two chromosomes: one large (2,961,146 bp) and one small (1,072,314 bp), encoding 3,885 open reading frames (ORFs). The majority of essential genes for cell functions and pathogenicity are located on the large chromosome, while the small chromosome contains a higher proportion of hypothetical genes and genes with origins other than γ-Proteobacteria. The small chromosome also harbors a gene capture system (integron island) and host 'addiction' genes typically found on plasmids, suggesting it may have originally been a megaplasmid captured by an ancestral *Vibrio* species. The genomic sequence provides insights into how a free-living environmental organism evolved into a significant human pathogen through horizontal gene transfer. Comparative genomics reveals asymmetrical distribution of genes between the two chromosomes, with the large chromosome containing more genes essential for growth and virulence. The small chromosome is enriched with hypothetical genes and genes of unknown function, possibly acquired through lateral gene transfer. The study also discusses the origin and function of the small chromosome, the transport and energy metabolism, interchromosomal regulation, DNA repair, and pathogenicity factors of *V. cholerae*.The study reports the complete genomic sequence of *Vibrio cholerae* El Tor N19691, a Gram-negative, γ-Proteobacterium with two circular chromosomes. The genome consists of two chromosomes: one large (2,961,146 bp) and one small (1,072,314 bp), encoding 3,885 open reading frames (ORFs). The majority of essential genes for cell functions and pathogenicity are located on the large chromosome, while the small chromosome contains a higher proportion of hypothetical genes and genes with origins other than γ-Proteobacteria. The small chromosome also harbors a gene capture system (integron island) and host 'addiction' genes typically found on plasmids, suggesting it may have originally been a megaplasmid captured by an ancestral *Vibrio* species. The genomic sequence provides insights into how a free-living environmental organism evolved into a significant human pathogen through horizontal gene transfer. Comparative genomics reveals asymmetrical distribution of genes between the two chromosomes, with the large chromosome containing more genes essential for growth and virulence. The small chromosome is enriched with hypothetical genes and genes of unknown function, possibly acquired through lateral gene transfer. The study also discusses the origin and function of the small chromosome, the transport and energy metabolism, interchromosomal regulation, DNA repair, and pathogenicity factors of *V. cholerae*.