Pacific oyster mortality syndrome affects juveniles of Crassostrea gigas oysters and threatens the sustainability of commercial and natural stocks of this species. Vibrio crassostreae has been repeatedly isolated from diseased animals and the majority of the strains have been demonstrated to be virulent for oysters. In this study we showed that oyster farms exhibited a high prevalence of a virulence plasmid carried by V. crassostreae while oysters, at an adult stage, were reservoirs of this virulent population. The pathogenicity of V. crassostreae depends on a novel transcriptional regulator, which activates the bidirectional promoter of a Type 6 Secretion System (T6SS) genes cluster. Both the T6SS and a second chromosomal virulence factor, r5.7, are necessary for virulence but act independently to cause to hemocyte (oyster immune cell) cytotoxicity. A phylogenetically closely related T6SS was identified in V. aestuarianus and V. tapetis, which infect adult oysters and clams, respectively. We propose that hemocyte cytotoxicity, is a lethality trait shared by a broad range of mollusk pathogens and we speculate that T6SS was involved in parallel evolution of pathogen for mollusks.