Vibrio harveyi, which is a Gram-negative marine bacterium, has emerged as a significant cause of disease in farmed greater amberjack Seriola dumerili in Japan. The symptoms of the bacterial infection included exfoliation of the head epithelium, ragged caudal fin, accumulated ascites, and ophthalmitis. We isolated V. harveyi strain GAN1807 in 2018 from diseased greater amberjack in Nomi Bay in Kochi Prefecture, Japan. We analyze the whole genome sequence of V. harveyi strain GAN1807. The draft genome sequence is annotated and is compared to those several foreign strains available in GenBank.