Bathypelagic samples collected during the global circumnavigation Expedition Malaspina 2010 were generated by amplifying the V4 and V5 hypervariable regions of the 16S rRNA gene using primers 515F-Y (5’-GTGYCAGCMGCCGCGGTAA-3’) and 926R (5'-CCGYCAATTYMTTTRAGTTT-3'). 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 bacterial diversity from bathypelagic samples and describe its biogeography.