Breeding of ornamental marine fishes was initiated in Makassar, South Sulawesi, Indonesia, to protect reef ecosystems from destructive fishing and to supplement income of local communities. However, stress associated with captive breeding conditions could enhance vulnerability of fish to disease. Wild-and captive-bred clownfish Amphiprion percula showed clinical signs such as white spots and warts typically associated with lymphocystis disease. Sequencing a portion of the DNA polymerase gene confirmed the identity of a lymphocystis disease virus (LCDV) in clownfish tissues that closely resembled LCDV from paradisefish; however, both strains were only 90% similar at the nucleotide level. Phylogenetic analysis suggests the LCDV is a new strain representing the first sequence of LCDV in A. percula. To determine the virus presence in clownfish and other ornamental marine species (OMS) in the hatchery, we developed conventional PCR and loop-mediated isothermal amplification (LAMP) assays that were comparatively sensitive at detecting the new LCDV strain. Among the PCR-tested clownfish, 19.4% (n = 14/72) were positive for the LCDV DNA that were either symptomatic or apparently healthy. Other OMS (n = 29) bred in the hatchery including seahorse Hippocampus spp., mandarin fish Synchiropus spp., and pajama cardinal fish Sphaeremia nepatoptera were negative by the LCDV PCR. The PCR and LAMP assays developed in this study will facilitate disease management by early detection of the LCDV and removal of potential reservoirs of the virus.