Marine fish populations have suffered the consequences of overfishing for a long time, leading to a loss in biodiversity. Traditional methods have been historically used to survey fish diversity but are limited to commercial species, particularly on the high seas. Environmental DNA (eDNA) has been successfully used to monitor biodiversity in aquatic environments. In this study, we monitored fish diversity in the Clarion–Clipperton Zone (CCZ) of the Eastern Pacific Ocean using eDNA metabarcoding. Our results identified 2 classes, 35 orders, 64 families, and 87 genera. The genera Mugil, Scomberomorus, and Scomber had high relative abundance in the mesopelagic and demersal zone. Fish diversity varied with sampling sites, and the greatest number of species was found at a depth of 2500 m. Environmental changes drove fish aggregation, and our results indicated that Chla was negatively correlated with fish communities, while DO was positively correlated with fish communities. This study released the fish diversity pattern and the effects of the environment in the CCZ, which would provide useful information for biodiversity management and an environmental baseline for the International Seabed Authority.
