Scallop aquaculture is of economic importance along the east coast of the tropical Pacific. However, scallop diseases have been observed and there is limited knowledge about bacterial pathogens, especially in hatcheries. The objective of this study was to identify and characterize one of the predominant bacteria in outbreaks of vibriosis that occurred in a scallop hatchery in south-central Ecuador. The strain SA-10GR was isolated from moribund veliger larvae of the scallop Spondylus limbatus. SA-10GR was identified as Vibrio rotiferianus by phenotypic characterization and whole genome sequence analysis. SA-10GR is a strain with lytic activity, susceptible to many antibiotics except amoxicillin (25 mu g), capable of producing siderophores and extracellular products with alkaline phosphatase, esterase, lipase esterase, leucine arylamidase, acid phosphatase, among others. The genome of V. rotiferianus consists of 5,579,217 bp; 5160 genes; 5086 protein-coding sequences (CDSs); 74 RNA genes (57 tRNA, 13 rRNA, and 4 ncRNA), and 40 pseudogenes. A total of six resistance genes vanT, adeF, E. coli parE, txR, CRP, and PBP3 were identified, and 110 virulence factors were detected. Functional characterization of SA-10GR shows extracellular products that cause damage to the fish model cell line (Epithelioma Papulosum Cyprini) and pathogenicity against larvae of the scallop Spondylus crassisquama and the oyster Magallana gigas (>= 86 % mortality at a concentration of 104 CFU mL-1 at 24 h post-challenge). Both species of larvae infected with the SA-10GR strain showed clinical signs of vibriosis. This study represents the first documentation of a Vibrio rotiferianus strain as a potential pathogen of two important cultured bivalve species along the Pacific coast, expanding the susceptible host range and geographic distribution for this Vibrio species.