Thraustochytrids have many desirable biomolecular and cellular properties for biotechnology applications: 1) a relatively simple level of cellular/genomic complexity; 2) a biochemical chassis that provides plentiful substrates for organic molecule biosynthesis; 3) a highly active PUFA synthase; 4) post-translational glycosylation profiles which are consistent with applications of recombinant proteins in mammals and 5) the ability to consume a diverse range of carbon sources. Thraustochytrid T18 is a commercially relevant source of docosahexaenoic acid (DHA). The three main fatty-acid species produced by T18 are C16:0, docosapentaenoic acid (DPA)-n6 and DHA. This strain has also been developed, in-house, as a biotechnology workhorse. The complete customization of lipid profiles in this prolific oil producing strain is a biotechnological goal at Mara. One of our strategies to meet this milestone includes engineering a classical pathway for fatty-acid synthesis in T18 to convert C16:0 into other, more complex, fatty acids. Advanced bioinformatics and basic molecular biology tools were combined to develop protocols for the manipulation of T18 and the engineering of both anabolic and catabolic pathways. Co-expression of multiple transgenes in T18, including fatty acid elongases and desaturases, using a 2A picornaviral system, results in recombinant strains producing high-value PUFAs.