Deep-sea subsurface habitats support novel and abundant microbial life. Recently, several studies have explored the phylogenetic diversity of microorganisms, mostly bacteria and archaea, in those environments. Viruses are key components of microbial assemblages, hence, the need to investigate them to better understand the deep biosphere’s ecology. In this study, we performed genomic analysis of 27 targeted flow cytometry-sorted viruses and 3 microbial cells from a one-milliliter hydrothermal fluid sample collected from IODP Hole U1362B CORK observatory at the Juan de Fuca Ridge (JFR) eastern flank. Preliminary results revealed a diverse viral community, as no two sorted viruses were identical to each other. The majority of predicted genes within the partially-sequenced viral genomes had no homology in databases. Phylogenetic analysis of the identified viral genes indicated that the viruses were most similar to large inducible lysogenic myoviruses. Additionally, the discovery of a cell from benthic group E (Euryarchaeota), a key member of the microbial community, containing a prophage in its genome supports the hypothesis that lysogeny is likely more pervasive than lytic infections in the deep biosphere. However, these results might reflect inherited flow cytometry and nucleic acids multiple displacement amplification biases toward large dsDNA viruses (e.g. myoviruses). On the other hand this approach allows investigating larger viruses typically removed by filtration in traditional metagenomics studies, and thus aids in providing a more complete picture of viral assemblages. This exploratory proposal is in line with two of the four C-DEBI research themes: Extent of Life, and Evolution and Survival.