Infectious spleen and kidney necrosis virus (ISKNV) belongs to the genus Megalocytivirus in the family Iridoviridae. This virus is the etiological agent of a serious and pandemic disease in fish. Cells infected with ISKNV undergo apoptosis. In this study, the ISKNV ORF005L gene was characterized and functionally investigated. Bioinformatics analysis revealed that the ORF005L protein contains a region similar to the catalytic domain of CTD-like phosphatases. Real-time quantitative-PCR results showed the transcription profile of ORF005L in ISKNV-infected cells; in these cells, ORF005L was initially transcribed at 24 h post-infection. The green fluorescent protein-tagged ORF005L protein was localized in the mitochondria. Sub-mitochondrial fractions were subjected to Western blot, and the results showed that ORF005L was specifically located in the inner membrane of the mitochondria. The ORF005L in fathead minnow cells was transiently expressed, resulting in the decrease in mitochondrial transmembrane potential, which induced cell apoptosis. ORF005L was knocked down by specific dsRNA, thereby significantly reducing the apoptosis of mandarin fish fry-1 cells induced by ISKNV infection. These results indicated that the ORF005L of ISKNV could disrupt mitochondrial function and cause apoptosis. This study may provide novel insights into the pathogenesis of Megalocytivirus infection.