We dissected the complete genome sequence of the O1 serotype strain Vibrio anguillarum 775(pJM1) and determined the draft genomic sequences of plasmidless strains of serotype O1 (strain 96F) and O2 (strain RV22) and V. ordalii. All strains harbor two chromosomes, but 775 also harbors the virulence plasmid pJM1, which carries the anguibactin-producing and cognate transport genes, one of the main virulence factors of V. anguillarum. Genomic analysis identified eight genomic islands in chromosome 1 of V. anguillarum 775(pJM1) and two in chromosome 2. Some of them carried potential virulence genes for the biosynthesis of O antigens, hemolysins, and exonucleases as well as others for sugar transport and metabolism. The majority of genes for essential cell functions and pathogenicity are located on chromosome 1. In contrast, chromosome 2 contains a larger fraction (59%) of hypothetical genes than does chromosome 1 (42%). Chromosome 2 also harbors a superintegron, as well as host "addiction" genes that are typically found on plasmids. Unique distinctive properties include homologues of type III secretion system genes in 96F, homologues of V. cholerae zot and ace toxin genes in RV22, and the biofilm formation syp genes in V. ordalii. Mobile genetic elements, some of them possibly originated in the pJM1 plasmid, were very abundant in 775, resulting in the silencing of specific genes, with only few insertions in the 96F and RV22 chromosomes.Vibrio anguillarum is a marine pathogen that causes vibriosis in close to 50 species of fish, including cultured and wild fish, mollusks, and crustaceans, in marine, brackish, and fresh water (1). Vibriosis is a hemorrhagic septicemia with dire consequences for fish rearing, especially in countries that depend heavily on fish for their food consumption. Despite the fact that V. anguillarum is a dramatic cause of vibriosis in fish, little is known about the genomic composition of this important pathogen. Although 23 serotypes have been reported in V. anguillarum, the O1 and O2 serotypes are the major causative agent of fish vibriosis (32,66,75). Many O1 serotype strains harbor 65-kb pJM1-type plasmids, which carry the siderophore anguibactin biosynthesis and transport genes, a main virulence factor of V. anguillarum, while one of the O1 serotype strains and other serotypes, such as all of the O2 strains, are plasmidless (1, 13, 33, 76). Many virulence factors have been characterized, but we are still far from getting the whole picture of the virulence mechanisms of this pathogen (1, 50). The fact that the pJM1 plasmid is an important component of virulence for the 775 strain but that the other three strains examined do not harbor this plasmid and are still virulent indicates that they must have different mechanisms to cause disease. Moreover, O1 serotype strains cause disease in salmonid fish, whereas O2 strains are usually isolated from cod and other nonsalmonids (1, 32, 43). We have previously performed random genome sequencing of V. anguillarum 775 genomic DNA and identified potent...