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VP51 and VP76 are two structural proteins of white spot syndrome virus (WSSV). However, there is some controversy about their localization in the virion at present. In this study, we employ multiple approaches to reevaluate the location of VP51 and VP76. Firstly, we found VP51 and VP76 presence in viral nucleocapsids fraction by Western blotting. Secondly, after the high-salt treatment of nucleocapsids, VP51 and VP76 were still exclusively present in viral capsids by Western blotting and immunoelectron microscopy, suggesting two proteins are structural components of the viral capsid. To gather more evidence, we developed a method based on immunofluorescence flow cytometry. The results revealed that the mean fluorescence intensity of the viral capsids group was significantly higher than that of intact virions group after incubation with anti-VP51 or anti-VP76 serum and fluorescein isothiocyanate conjugated secondary antibody. All these results indicate that VP51 and VP76 are both capsid proteins of WSSV.