Although the abundance, diversity and evolution of viruses in surface marine environments are well recognized, little is known in general about the structure and evolution of deep-sea viruses, and a few genomes from virus isolates or metagenomics from deep-sea environments are available to date (Anantharaman et al 2014; Julien et al., 2015). The glaring paucity of reference genomes from viruses representing abundant and/or relevant viral population hinders the study of the biology and ecology of deep viral assemblages. In the present work, we will demonstrate the power of a new omic approach, Single Virus Genomics (SVG) to unveil unknown and uncultured viruses recovered directly without cultivation from the Mediterranean Sea (mesopelagic: 25 and 75 m; deep-sea: 1000 and 2000 m) and from samples taken during the Malaspina expedition in the North Atlantic (4000 m depth) and the Pacific Ocean (2000 m). A total of 7,968 single viruses were sorted by fluorescence activated sorting. So far, whole genome amplification by multiple displacement amplification yielded a total of ≈500 single amplified viral genomes (SAvGs), and 132 SAvGs from mesopelagic and deep-sea have been sequenced by Illumina technology. This study, for the first time, opens the door of new ways to explore the uncultured viruses and leads to a unique and valuable genome datasets of reference genomes to compare with metaviromes, metagenomes and traditional virus isolates.