The Marine Microbial Eukaryote Transcriptome Sequencing Project was a collaboration between the National Center for Genome Resources, the Gordon and Betty Moore Foundation's Marine Microbiology Initiative, and the international marine microbial eukaryote research community to sequence the transcriptomes of approximately 700 samples from hundreds of diverse organisms. Marine microbial eukaryotes are found in all major eukaryotic branches of the evolutionary tree. They perform a diverse range of functions in marine ecosystems, including photosynthesis, predation, and parasitism. Despite the great abundance of microeukaryotes in the ocean, their importance as absorbers of carbon dioxide and their critical contribution to marine food webs (among many ecological roles), the gene content of these microorganisms is only beginning to be explored because their genomes can be structurally complex and can be many gigabases in size. This program was intended to increase the research community's baseline of scientific knowledge by creating catalogs of genes that suggest how these organisms thrive in diverse marine habitats and how they influence marine ecosystems, biogeochemical cycles, and the composition of the atmosphere. Transcriptome datasets are complex and should be approached with awareness, especially in light of the very deep Illumina sequencing used to generate these data. While many researchers attempted to provide axenic and uni-algal total RNA extracts for sequencing, it did not always turn out to be that way. The deep Illumina sequencing may have occasionally picked up very low levels of non-target RNA, and low levels of bacteria may have been present but not known to the laboratory that provided the sample. For additional project information, details about the varied samples, and data, including transcriptome assemblies and annotations, please see: http://marinemicroeukaryotes.org/ and http://camera.calit2.net/mmetsp/.