AIM: Cholera remains an endemic disease in Bangladesh and recently, the severity of the disease has significantly increased in urban area since the emergence of the new variant of Vibrio cholerae O1 El Tor. In this study, Whole Genome Sequencing (WGS) was utilized to investigate the current genomic profile of V. cholerae O1 strains, isolated from symptomatic patients in the low-income urban area of Arichpur, Dhaka, Bangladesh. METHODS: During October 2015, three V. cholerae O1 strains (VC-1, 2 and 3) were isolated from rectal swabs of two patients living in households 588 m apart. One of the two patients was co-infected with two V. cholerae strains (VC-1 and VC-3). Major virulence factors, biotype and antimicrobial resistance genes were identified by WGS. A global phylogenetic tree was inferred using genome wide SNPs (Single Nucleotide Polymorphism) analysis. RESULTS: All the V. cholerae strains were El Tor variant of Vibrio cholerae O1 carrying ctxB1 (standard classical genotype). SNP based global phylogeny revealed that these isolates are strictly clonal and the closest neighboring genomes were epidemic clones of V. cholera O1 from Pakistan isolated in 2010. 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 in silico MultiLocus Sequence Typing (MLST) revealed that these strains belonged to sequence type 69. CONCLUSION: 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.