There are an estimated 1030 viruses in the world oceans, the majority of which are phages (viruses that infect bacteria). Extensive research in surface marine environments has demonstrated the significant influence of marine phages on microbial communities. But the dark ocean is the largest and the most unexplored habitat in the biosphere, comprising 1.3 X 1018 m3. Accordingly, evaluating the role of viruses in the deep ocean remains an elusive, but pivotal underpinning of our growing understanding of the microbial oceanography of the open and dark oceans. During the Malaspina-2010 circumnavigation cruise along the Global and Subtropical Ocean, the analysis of bacterial metagenomes from deep ocean and the fragment recruitment analyses of available prokaryote genomes against the deep ocean bacterial metagenomes revealed that Alteromonas genomes are highly abundant and ubiquitous in most of the metagenomes. Also based on prokaryotic OTUs abundance by iTAGs (16S rRNA amplicon fragments) Alteromonas was the first most abundant OTU. With these preliminary results, the study of the phage-bacteria interactions based on Alteromonas strains would be interesting to understand the viral ecology on deep waters. In this context, we isolated and sequenced 17 phages infecting Alteromonas sp. strains from deep waters in the Mediterranean Sea. This comparative analysis of multiple phages retrieved from a single bacterial species offers an opportunity to evaluate the heterogeneity of their genomic structure and functional diversity. Moreover, viral metagenomic comparisons were carried out to elucidate their distribution in natural aquatic systems and explore putative biogeographic patterns.