The Clarion Clipperton Zone (CCZ) has attracted growing commercial interest because of its huge reserves of polymetallic nodules and has therefore become an important seabed area for global biodiversity conservation. Foraminifera, significant members of abyssal benthic communities, have been listed as an object of environmental assessment in the specification ISBA/25/LTC/6 issued by the International Seabed Authority due to their high sensitivities to environmental conditions. However, previous ecological studies of CCZ foraminifera were mainly based on morphological analysis and rarely on DNA sequences. Here, we obtained the first DNA metabarcoding dataset of foraminifera in the western CCZ using high-throughput sequencing technology and focused on the diversity and distribution of hard-shelled foraminiferal assemblages, which have excellent fossil records on the seafloor and are widely used for paleoenvironmental reconstructions.