These DNA metabarcoding data derive from zooplankton collected within the abyssal benthic boundary layer (BBL) in the eastern Clarion Clipperton Zone (NORI-D exploration claim). Zooplankton was collected using in-situ plankton pumps mounted on an autonomous benthic lander during 2 cruises: Fall and Spring 2021. 1/4 of the material collected on each deployment (1/2 of PumpA) was PCR amplified for mtCOI, 18S V1-V2, and 18S V7-V8 and sequenced on an Illumina MiSeq run (300-bp, paired-end).