Biofouling is the colonization of various aquatic organisms (e.g., bacteria, algae, barnacles, mussels, etc.) on the submerged surface of ship hulls and artificial surfaces of mariculture equipment and floating platforms, causing major economic loss and environmental impacts. However, most studies have focused on bacteria. Here, we evaluated the usefulness of eDNA metabarcoding platform for monitoring of biofouling animals. To monitor seasonal variation of biofouling animals, animal attachment on the four plates equipped at the cage aquaculture of Jangmok. Metabarcoding approach targeting the cytochrome c oxidase subunit 1 (COI) gene was employed to investigate invertebrate and specific Urochordata communities on the plate or seawater for comparison. We identified experimentally that eDNA analyses increased detection of species by more than 90% compared to conventional PCR method. Especially, we obtained all of the Phylum level that detected from PCR. The eDNA approach was very useful to identify undetectable animals when we directly compare the samples with conventional PCR method. Relatively high percentage of unclassified taxa are remained to be resolved with further study phylum-specific primer sets. Taken together, these results can contribute to understand seasonal blooming of biofouling animals and suggest usefulness of eDNA metabarcoding approach.