A high mortality of the Yesso scallop Patinopecten yessoensisis (Jay, 1857) larvae occurred during the seedling process: the larvae lost their ability to swim, their cilia fell off and their valves closed, they then sank to the bottom of the nursery pond and died. Total viable vibrio's counts in moribund larvae were 1.1 × 10⁴ colony forming unit/g on tryptone-citrate-bilesucrose agar plates. Two dominant strains, named V1 and V2, accounted for 64.3% and 32.1% of total vibrios counts, respectively. Strain V1 exhibited beta hemolysis, whereas V2 exhibited alpha hemolysis. A challenge test showed that the signs of infected larvae were identical to those of natural moribund larvae, and the cumulative mortality caused by strains V1 and V2 was significantly higher than that of the control (P < 0.05). Strains V1 and V2 shared 99.9% and 99.2% identity with Vibrio splendidus ctt 31/5 and Vibrio tasmaniensis 007, respectively, by 16S rDNA sequencing. The presence of genes coding for virulence factors was examined by PCR analysis, showing that strain V1 possesses the extracellular metalloprotease (vsm) gene. In this study, strains V1 and V2 were demonstrated to be pathogens causing mortality in Yesso scallop larvae.