With the sampling limitations for the study of the hadopelagic environment, an alternative in the use of sediment eDNA is utilized in one of the world’s most productive ecosystems: The Atacama Trench. Having a history of overfishing events and effects of ENSO of differing intensities, five sites were sampled through sediment cores at depths going from 2400 to nearly 8000m. As layers of sediment are formed over time, within each layer are fragments of eDNA deposited by the pelagic fauna that inhabited at that time. For this study, the sediment layers were dated and the community composition for the years in which they inhabited was determined utilizing metabarcoding with the Euka02 and 18SMini primers. The communities identified for both primers are mainly composed of chordates and members of the recently established Chromista kingdom, and through further beta-diversity analyses, are shown to not be too distinct from one another. Alphadiversity was calculated for all sites in intervals of 15 years, and it became clear that there was a drop in biodiversity from 1977 to 2002. This is attributed to human influence, as the extensive fishing efforts in this period of time combined with the escape of salmonids from farms and adverse ENSO events contributed to the reduction of diversity, warning that although diversity is currently back at previous levels, anthropogenic impacts must be limited for conservation purposes. Overall, it is shown that sediment eDNA is a valuable emerging tool not only for research on the current state of communities in pelagic environments, but also as a snap-shot of the past that allows for comparisons within an ecosystem.