Bathypelagic samples collected during the global circumnavigation Expedition Malaspina 2010 were generated by amplifying the 18S rRNA gene using primers XXXXX and XXXX. Sequencing was performed in an Illumina MiSeq platform (iTAGs) using 2x250 bp paired-end approach at Genoscope. The data generated has been used mainly to describe the eukaryotic diversity from bathypelagic samples and describe its biogeography.