Abstract: Overfishing, leading to the loss of biodiversity, has a long-lasting negative influence on marine fish communities. Traditional methods used to survey fish diversity are largely limited to commercial species in the high sea. However, environmental DNA (eDNA) has been successfully used to monitor the biodiversity in aquatic environments. In this study, we used eDNA metabarcoding technology and fish universal primers (MiFish, COⅠ) to monitor the fish diversity before mining in the Clarion-Clipperton Zone of the eastern Pacific Ocean. As results, 140 genera, 132 fishes were detected and their detecting rate decreased with water depth. A total of 88 genera, 62 families, 35 orders, 2 classes, 57 fish species were identified by MiFish primers. A total of 72 genera, 57 families, 29 orders, 2 classes, 87 fish speies were identified by the COⅠ primers. Based on COⅠ metabarcoding technology, endangered species (Anguilla japonica, Anguilla rostrata, Himantura uarnak, Mobula tarapacana), critically endangered species (Anguilla anguilla), vulnerable species (Makaira nigricans, Pomatomus saltatrix) and near threatened species (Prionace glauca) have been detected. Based on MiFish metabarcoding technology, near threatened species (Prionace glauca, Harpadon nehereus, Scoliodon laticaudus) and a vulnerable species (Epinephelus fuscoguttatus) are detected. The number of genera or family detected by MiFish primers are higher than that of COⅠ primers, and the MiFish primer pair has efficient on the OTU of genera or family coverage and species resolution. Results show that eDNA metabarcoding technology can effectively identify fish species. It shall play important role in monitoring marine fish diversity in future. As a non-invasive method, fish diversity monitored by eDNA metabarcoding is much higher than that captured by stereo-video lander system. Meanwhile, eDNA metabarcoding based on MiFish primers has more advantages in monitoring fish species.