These data consist of the raw amplicon DNA sequence files from three primer sets targeting eukaryotic diversity in environmental DNA of deep-sea water samples collected along the mid-Atlantic coast as part of the DEEP-SEARCH project. One marker targeted an approximately 120 bp portion of nuclear 18S rRNA (samples with 18S in their name), another targeted a 313 bp portion of the mitochondrial cox1 gene (samples with cox1 in their name), and another targeted an approximately 120 bp portion of the mitochondrial 16S gene (samples with 16Smet in their name). Water samples were collected from different deep sea habitat types including cold seeps and cold water coral reefs using two Niskin bottles attached to an ROV. Two methods of filtration were used, which included one liter of water filtered through a 0.2 micron Sterivex filter, or ten liters of water through a 0.8 micron cellulose acetate filter. Sterivex filters have "sterivex" and/or "1L" in their name, whereas the ten liter samples have "10L" and or "PF" and/or "prefilter" in their name. To differentiate the two Niskins used on the ROV, they were given the names "Darya" and "Sedna". The purpose of this experiment was to characterize eukaryotic diversity among these habitats through eDNA metabarcoding.