Vibrio, cholerae is the aetiological agent of the deadly diarrhoeal disease cholera. In this study the 7(.)5 kb Vibrio seventh pandemic island-II (VSP-II) that is unique to V. cholerae El Tor and 0139 serogroups was analysed and it was found to be part of a novel 26(.)9 kb genomic island (GEI) encompassing VC0490-VC0516. The low-GC-content VSP-II encompassed 24 predicted ORFs, including DNA repair and methyl-accepting chemotaxis proteins, a group of hypothetical proteins and a bacteriophage-like integrase adjacent to a tRNA gene. Interestingly, V. cholerae ORFs VC0493-VC0498, VC0504-VC0510 and VC0516, which encodes an integrase, were homologous to Vibrio vulnificus strain YJ016 ORFs VV0510-VV0516, VV0518-VV0525 and VV0560, which also encodes an integrase, respectively. Some ORFs showed amino acid identities greater than 90% between the two species in these regions. In V. vulnificus strain YJ016, a 43(.)4 kb low-GC-content (43%) GEI encompassing ORFs VV0509-VV0560 was identified and named V. vulnificus island-I (VVI-I). The 52 ORFs of VVI-I included a phosphotransferase system gene cluster, genes required for sugar metabolism and transposase genes. There was synteny and homology between the 5' region of V. cholerae VSP-II and the 5' region of V. vulnificus VVI-I; however, VVI-I contained an additional 31(.)5 kb of DNA between VV0526 and VV0560 in strain YJ016. A second V. vulnificus strain, CMCP6, did not contain the 43(.)4 kb VVI-I; in this strain two ORFs were found between the 5' and 3' flanking genes VV10636 and VV10632, showing 100% identity to VV0508 and VV0561, respectively, which flank VVI-I.