Whole Genome Sequencing (WGS) was utilized to investigate the genomic profile of Vibrio cholerae O1 strains, isolated from symptomatic patients in a low‐income urban area of Dhaka, Bangladesh. Comparative genomics using bioinformatics tools were applied to identify major virulence factors, biotype and antimicrobial resistance genes in three V. cholerae O1 strains (VC‐1, 2 and 3) isolated from two case patients. A phylogenetic SNP (Single Nucleotide Polymorphism) based analysis was conducted to infer the relatedness to V. cholerae O1 strains isolated elsewhere. The V. cholerae strains were the El Tor variant carrying ctxB1 (standard classical genotype). SNP based global phylogeny revealed that the three isolates were strictly clonal and the closest neighboring genomes were epidemic clones of V. cholerae O1 isolated in 2010 from cholera patients in Pakistan. All strains harbored the integrase gene of the SXT element (intSXT), antimicrobial resistance genes for aminoglycosides, phenicol, sulphonamide, and trimethoprim except VC‐1 that lacked sulphonamide resistance genes. The Multilocus Sequence Typing (MLST) revealed that the strains belonged to sequence type, ST69. The study provides knowledge on current genetic traits of clinical V. cholerae O1 circulating in urban household clusters of Bangladesh which may help in predicting emergence of new pandemic strains in Bangladesh.