Viruses are ubiquitous and the most numerous biological entities in the ocean. The genetic diversity of marine viruses appears to be immense, yet there is agreement that much of that diversity remains to be discovered. The assessment of viruses’ global role modulating microbial mortality, evolution, and metabolic reprogramming, as well as their impact on biogeochemical cycles in the marine environment is precluded by our still limited knowledge of viral diversity and global distribution. Pragmatically, marine viruses are difficult to investigate. Their diverse capsid morphologies and sizes and genome nature (i.e., single-stranded and double-stranded DNA or RNA) hinder the development of a single method for studying all viruses within a natural assemblage. In addition, virus studies are challenged by the absence of a universal genetic marker for taxonomic identification and molecular quantification. This talk will highlight some breakthrough discoveries facilitated by single virus genomics and targeted viromics about viral diversity and community connectivity from surface to deep ocean waters and into the deep-sea subsurface.