Marine viruses are key components of marine microbial communities, as they influence the cellular abundances and the community structure of microbes, participate in their genetic exchange, and intervene in the ocean biogeochemical cycles. Most studies dealing with the role of viruses in the marine environment have been done from a bulk community point of view, but going from the bulk community perspective to specific virus-host relationships is essential in order to understand the role of viruses in shaping a determined host community, in modifying host genomes, and ultimately in the release of organic compounds from the lysed cells. For this reason, in this thesis we implemented and applied different methodologies that are able to detect, visualize and quantify virus-host interactions in marine eukaryotes at the single cell level. We focused on picoeukaryotes (cells <3μm) because they play crucial roles in marine food webs and biogeochemical cycles, and virus-host interactions in natural populations of these minute eukaryotes are largely unknown. In the first chapter we combined previously developed techniques, used to assess prokaryotic host-phage interactions, to implement VirusFISH for detecting specific virus-host dynamics, using as a model system the photosynthetic picoeukaryote Ostreoccocus tauri and its virus OtV5. With the VirusFISH technique, we could also monitor the infection, as well as quantify the free viruses produced during the lysis of the host in a non-axenic culture, which allowed the calculation of the burst size. This study set the ground for the application of the VirusFISH technique to natural samples. In the second chapter of this thesis, we applied VirusFISH to seawater samples from the Bay of Biscay (Cantabrian Sea) to study the dynamics of viral infection in natural populations of Ostreococcus along a seasonal cycle. We were able to quantify the percentage of cells infected over time, and compared these results with the transcriptional viral and host activities derived from metatranscriptomic data. This constitutes the first study where a specific viral-host interaction has been visualized and monitored over time in a natural system. Picoeukaryotes in the ocean are prevalently uncultured, and thus, in the third chapter of this thesis we went an step further to unveil novel viral-host relationships in eukaryotic uncultured hosts. For this purpose, we mined single amplified genomes (SAGs) of picoeukaryotes obtained during the Tara Oceans expedition for viral signatures. We found that almost 60% of the cells analyzed presented an associated virus with narrow host specificity. Some of the viral sequences were widely distributed and some geographically constrained, and they were preferentially found at the deep chlorophyll maximum. Moreover, we found a mavirus virophage potentially integrated in four SAGs of two different lineages, suggesting the presence of virophages is more common than previously thought. In summary, in this thesis we have implemented and used techniques that allow us to detect and monitor specific virus-host interactions, which is one of the major challenges in marine viral ecology. On the one hand, VirusFISH arises as a powerful technique that can be easily adapted to any host-virus system that has been genome-sequenced. On the other hand, the results obtained with the single cell genomics offer the opportunity to formulate hypothesis based on detected viral-host interactions in uncultured prevalent marine picoeukaryotes, which can be later tested using experimental approaches