Uncovering and understanding the biological diversity of the deep ocean realm remains as a pending and challenging task. Here, we used the metabarcoding approach to assess the diversity of zooplankton from the upper 1,000 m down to abyssopelagic depths (5,000 m), above the Atacama Trench in the southeast Pacific. A high deep-sea diversity of zooplankton was found, even higher than that of the upper layer, and highly structured zooplankton assemblies across the vertical axis, with a maximum species richness at mid depths (1,000 and 2,000 m), and more than 50% of unknown species.