Coccolithoviruses are giant double stranded DNA virus that infect Emiliania huxleyi, the most abundant coccolithophore in the oceans. After a review on the current knowledge existing on this host/viral system, the author presents a series of approaches conducted to unveil functional genomic features that characterize that system. Evidence for the transfer of 29 genes between E. huxleyi’s and the EhV genomes is presented. In particular, seven genes involved in the unique viral sphingolipid biosynthesis pathway encoded in EhV genome. Then focusing on natural coccolithovirus populations, transcription dynamics of both host and virus are presented, along with a clear demonstration of coccolithovirus community take over during E. huxleyi’s blooms. Novel transcription features associated with EhV infection are described, namely the utilization of genes potentially related to genetic information processing, posttranslational control, intracellular trafficking mechanisms, and control of programmed cell death. Finally the author discusses the potential implications of these findings and future research perspectives in the plankton virology field.