The samples reported here are from 15 depths (50 - 2000m) across the water column of the Black Sea western gyre. Suspended particulate matter was collected on 9-10 June 2013 with in situ pumps on pre-combusted glass fiber filters with 0.7 um pore size. Unamplified DNA was sequenced with Illumina Miseq. The 15 metagenomes were cross-assembled and binned to form metagenome assembled genomes (MAGs). This project is a collaboration between the Royal Netherlands Institute for Sea Research and Utrecht University.