Members of the kingdom protista are believed to be earth’s first eukaryotes. The concept of their evolution and relationship have been changing as new protists are continuously being discovered. Marine microbial eukaryotes comprise a vast array of single-celled, nucleated microbes, including diatoms, dinoflagellates, amoeba, ciliates and water molds. These organisms fill numerous ecological roles ranging from photosynthetic primary producers (base of aquatic food webs) to heterotrophic consumers of pre-formed organic compounds. Phytoplankton is responsible for generation of up to half of the world’s oxygen. Despite their great abundance and importance, the gene content of oceanic microbial eukaryotes has not been studied extensively. Therefore one of the major goals of MMETSP is to generate a catalogue of expressed genes from 750 such microbes. So far 688 samples representing 315 unique species have been approved for sequencing, assembly and annotation. 38 TruSeq RNA libraries have already been sequenced from both ends (100-nt reads) on the Illumina Hi-Seq 2000 platform, assembled and annotated based on searches against the PFam, SUPERFAMILY, and TIGRFAMs HMM libraries. All sequence reads will be deposited to ENA (European Nucleotide Archive) while the assemblies, annotations and metadata will be made available through CAMERA (camera.calit2.net). Primary focus of this project is to increase the research community’s scientific knowledgebase and also improve metagenomic analyses of complex marine communities. For more details, please visit the project web site MarineMicroEukaryotes.org. This project is funded by the G.B. Moore Foundation (www.moore.org).