Iridovirus is a serious aquatic virus infecting variable species of fish and frog. Development of a rapid, reliable detection method is an important issue for commercial and scientific purposes. With specific anti-body-functionalized magnetic nanoparticles, viruses can be bound immunologically and quantitatively detected by measuring the related magnetic signals. Immunomagnetic reduction (IMR) is a technique to measure the magnetic signals change in this work. Using this assay, the low-detection limit of iridovirus was found 101 TCID50/mL. There was no significant interference from the other grouper viruses including nervous necrosis virus (NNV). The iridovirus concentration in grouper detected with IMR was 19% related to real-time polymerase chain reaction (real-time PCR). These results demonstrated the feasibility of IMR on iridovirus screening in grouper.