Fish that live in mesophotic ecosystems are not well documented. Even though certain fish species may be exclusive to mesophotic or shallow-water ecosystems, mesophotic ecosystems may serve as an essential refuge for some species. We will specifically investigate whether fish biodiversity from mesophotic reef zones follows the same patterns as fish in the photic zone by comparing the biodiversity of marine fish in mesophotic and shallow water ecosystems in Indonesia using eDNA metabarcoding.