Marine protists are an important part of the ocean ecosystem. They may possess unique sets of biosynthetic pathways and, thus, be promising model organisms for metabolic engineering for producing substances for the pharmaceutical, cosmetic, and perfume industries. Currently, full-genome data are available just for a limited number of protists hampering their use in biotechnology. We characterized the morphology of a new cultured strain of Thraustochytriaceae isolated from the Black Sea ctenophore using phase-contrast microscopy. Cell culture was performed in the FAND culture medium based on fetal bovine serum and DMEM. Phylogenetic analysis was performed using the 18S rRNA sequence. We also conducted a transcriptome assembly and compared the data with the closest species. The protist belongs to the genus based on the 18S rRNA sequence analysis. We designated the isolated protist as . The closest species with the genome assembly is . Transcriptome analysis revealed the majority of the fatty acid synthesis enzymes. Our findings suggest that the is a promising candidate for biotechnological use. Together with the previously available, our data would allow the establishment of an accurate phylogeny of the family Thraustochytriaceae. Also, it could be a reference point for studying the evolution of the enzyme families.