Vibrio harveyi is an important aquaculture pathogen that can infect a large number of marine animals. In this study, we examined three V. harveyi strains (VJ1, VJ2, and VJ3) isolated in the years of 2008, 2009, and 2010 respectively from diseased Japanese flounder ( Paralichthys olivaceus) in a fish farm in China that had been inflicted with disease outbreaks. VJ1, VJ2, and VJ3 exhibited comparable virulence in a flounder model and induced symptoms in experimentally infected fish that are indistinguishable from those of naturally diseased fish. 16S rDNA and multilocus sequence analysis indicated that VJ1, VJ2, and VJ3 share 98–100% sequence identities with known V. harveyi isolates in 16S rDNA and four housekeeping genes. VJ1, VJ2, and VJ3 have distinct and identical AFLP banding patterns, which differ profoundly from those of two environmental V. harveyi isolates. VJ1, VJ2, and VJ3 exhibited comparable growth profiles and hemolytic activities and possess the vhh hemolysin gene. Compared to an environmental isolate, VJ1, VJ2, and VJ3 showed comparable and significantly stronger resistances against the bactericidal effect of host serum and induced higher levels of respiratory burst activity in head kidney macrophages. However, VJ1, VJ2, and VJ3 were unable to proliferate in macrophages. When incubated with a cultured cell line of flounder, VJ1, VJ2, and VJ3 induced apoptosis characterized by the occurrence of DNA fragmentation, apoptotic bodies, and elevated caspase 3 activity. Taken together, these results indicate that VJ1, VJ2, and VJ3 are probably clones of the same V. harveyi lineage that has persisted during the examined three-year time frame and likely caused recurrent disease outbreaks via a virulence mechanism involving serum resistance and triggering apoptosis in host cells.