Thirty-four Vibrio cholerae isolates collected from a cholera outbreak in Hyderabad, South India were found to belong to serogroup O1 biotype El Tor serotype Ogawa. The genotype of all the isolates was confirmed by PCR assays. All the isolates were found PCR positive for ctxAB, ompW, rfbO1, rtxC, and tcpA genes. All the isolates but one harboured $rstR^{El;Tor}$ allele. However, one isolate carried both $rstR^{El;Tor}$ as well as $rstR^{Classical}$ alleles. Cholera toxin (ctxB) genotyping of the isolates confirmed the presence of altered cholera toxin B of classical biotype in all the isolates. All the isolates except VCH35 harboured an RS1-CTX prophage array on the large chromosome. The isolate VCH35 contained a tandem repeat of classical CTX prophage on the small chromosome. The clonal relationship among the V. cholerae isolates as carried out by enterobacterial repetitive intergenic consensus sequences PCR, BOX PCR and randomly amplified polymorphic DNA, uniformly showed a genetic relationship among the outbreak isolates. The results of this study suggest that altered El Tor biotype V. cholerae with the classical cholera toxin gene are involved in cholera outbreaks in India.