This study was undertaken to analyze the cholera situation during July to November 2000 six month after the super-cyclone in saline tract of Orissa, India. Hundred ninety eight rectal swabs collected from hospitalized diarrhoea cases were subjected for bacteriological analysis. Of the 162 culture positive cases, V.cholerae 81 (50%), EPEC 1 (0.6 %), EHEC 3 (1.8%), EAggEC 2 (1.2%), Shigella flexneri 3 (1.8%) and Salmonella spp. 4 (2.5%) were isolated. Quadriplex and monoplex PCR assay revealed that, 51(31.5%) were V. cholerae O1 and 30 (18.5%) V. cholerae O139; carried ctxA, tcpA (Biotype El Tor), zot, ace and toxR except 3 V. cholerae O139 negative for ctxA gene. Incidence of V. cholerae six month after the super cyclone was found significantly higher than the pre-cyclonic period (P < 0.5). Strains of V. cholerae O1 was observed to be resistant to nalidixic acid, furazolidone, streptomycin, co-trimoxazole, ampicillin & neomycin. Except for co–trimoxazole, the resistant pattern of O139 was identical with that of O1 strains.  The study revealed that V.cholerae O1 & O139 were the potential organism for cholera outbreaks in coastal Orissa, where ctxA & tcpA genes played a major role for pathogenesis. Incidence and emergence of fluroquinolone resistant V. cholerae O1 and O139 and nalidixic acid resistant O139 sero group should be closely monitored.