Emiliania huxleyi is the most prominent modern coccolithophore, a group of marine unicellular eukaryotes that play a critical role in ocean biogeochemistry. Coccolithoviruses are large double stranded DNA viruses, which is responsible for the demise of large oceanic blooms formed by E. huxleyi. E. huxleyi virus (EhVs) acquired a series of enzyme-coding genes predicted to be involved in the sphingolipid biosynthesis by horizontal gene transfer between virus-host. Currently, there is limited experimental validation identifying the functions of these genes in EhV. Genetic transformation of eukaryotic cells is a powerful tool to get an insight into gene functions of the studied organisms. Serine palmitoyltransferase (SPT) catalyzes the first committed step in de novo sphingolipid biosynthetic pathway. Here, a novel vector system for the transformation of E. huxleyi was designed. It contained fragments of promoter and terminator sequences of E. huxleyi endogenic fucoxanthin chlorophyll a/c-binding protein gene “fcp” and harbored EhV-99B1 spt gene. The resultant recombinant transformation vectors pEhux-I-spt and pEhux-II were co-transferred into E. huxleyi BOF92 by electroporation. Transformants were obtained upon glufosinate-ammonium selection, and confirmed by Southern hybridization, genome PCR, qRT-PCR and Western blot screening of spt gene, which indicated that spt gene was integrated into the nuclear genome and was expressed at the mRNA and protein levels. The expression of the viral spt gene led to differences in lipid compositions analyzed using thin-layer chromatography (TLC). The results present the genetic transformation system for E. huxleyi, providing additional genetic resource with potential for exploring basic biological questions such as the virus-host interactions.