Acute hepatopancreatic necrosis disease (AHPND) is caused by infection with Vibrio parahaemolyticus. In this study, five strains of V. parahaemolyticus were isolated from Litopenaeus vannamei with AHPND. The primer set AP2 targeting the plasmid harbored in AHPND-causing V. parahaemolyticus (VPAHPND) was used in the PCR amplification, and it was found that all five isolates carried the AHPND related plasmid. Mitomycin C was used to induce and screen the lysogenic phages in VPAHPND isolates. The growth curves showed that two isolates of V. parahaemolyticus, 20130629002S01 and 20130726001S01, contained lysogenic phages. Phage 1 and Phage 2 were released from 20130629002S01 and 20130726001S01 respectively after the induction with 0.5 μg/ml mitomycin C. Transmission electron microscopy revealed that Phage 1 had a tailed shape and Phage 2 had a spherical shape. The challenge test on Artimia nauplii suggested that the virulence was significantly different between the 5 strains of V. parahaemolyticus. The pathogenicity of two lysogenic phages-containing strains, 20130629002S01 and 20130726001S01, was significantly lower than that of phage-free 20130721001S02. Our study suggested that the presence of lysogenic phage might not necessarily correlate with the pathogenicity of the host bacterium V. parahaemolyticus.