Coccolithophores are one of the most widespread groups of unicellular eukaryotic marine phytoplankton and play crucial roles in marine ecosystem. Some coccolithophores are bloom-forming species in ocean and offshore. In natural marine ecosystem, virus infection is one of the major causes of natural mortality and the demise of large oceanic blooms formed by this group. Integrated analysis based on the genomic sequences of Emiliania huxleyi, a major species of coccolithophores and its specific lytic virus Emilliania huxleyi virus (EhV), has implied that EhV obtained a series of key enzyme genes involved in sphingolipids metabolism from host genome by horizontal gene transfer. In some ways, EhV manipulates sphingolipids metabolism of host and triggers biosynthesis and accumulation of infection-derived sphingolipids, resulting in the apoptosis of host cell. Thus, virus-mediated host sphingolipids metabolism plays an important role in virus-host interaction. Here, we describe the horizontal gene transfer between EhV and host, the characteristics of virus-mediated host sphingolipids metabolism and the ecological significance in order to understand the complicated interaction between E. huxleyi virus and its host.