The phenotypic and genotypic characteristics of 6 clinical strains of Vibrio cholerae isolated in Surabaya, Indonesia in 2009 were examined. The DNA fingerprints obtained suggested that these isolates were not from a single clone. Furthermore, all isolates produced cholera toxin and possessed the classical type of toxin B subunit gene, thus meaning that this is the first report of the occurrence of El Tor variants of V. cholerae in Indonesia. Although all isolates were sensitive to almost all antibiotics tested, including ampicillin, chloramphenicol, ciprofloxacin, gentamicin, levofloxacin, kanamycin, nalidixic acid, norfloxacin, streptomycin, trimethoprim-sulfamethoxazole, and tetracycline, and had no mutation in the gyrA and parC genes, they nevertheless possessed the class 1 integron that is a molecular vehicle for the acquisition of antibiotic resistance genes, suggesting that they have the potential to acquire the genetic element for drug resistance.