Megalocytivirus is a genus of piscine viruses that belongs to the Iridoviridae family, and this family comprises red seabream iridovirus (RSIV), turbot reddish body iridovirus (TRBIV), and infectious spleen and kidney necrosis virus. RSIV causes high mortality and economic losses in the rock bream (Oplegnathus fasciatus) Korean aquaculture industry. The World Organization for Animal Health’s Office International des Epizooties has provided a manual for RSIV detection. However, detection against TRBIV has not been confirmed. In this study, a multiplex PCR method was established to detect two genotypes of Megalocytivirus, RSIV and TRBIV. New primer pairs were optimized for the PCR reaction. A mixture of one universal and two specific primer pairs could amplify three distinct products targeting three different genes. The sensitivity of the primer pairs was evaluated and results showed a detection limit of 2.0  105 copies for each target gene. Moreover, the primer pairs did not amplify any other viruses. The evaluation of multiplex PCR using 21 RSIV Korean isolates has shown that it can distinguish two genotypes of Megalocytivirus from 21 RSIV Korean isolates. Finally, we describe a new multiplex PCR method to detect different genotypes of Megalocytivirus simultaneously, which makes the diagnosis of viral diseases occurring in the Korean aquaculture industry more convenient.