Gas chromatographic profiling of fatty acids was performed during the growth cycle of four marine microalgae in order to establish which, if any, of these could act as a reliable source of genes for the metabolic engineering of long chain polyunsaturated fatty acid (LC-PUFA) synthesis in alternative production systems. A high-throughput column based method for extraction of triacylglycerols (TAGs) was used to establish how much and at what stage in the growth phase LC-PUFAs partition to storage lipid in the different species. Differences in the time course of production and incorporation of docosahexaenoic acid (22:6n-3, DHA) and eicosapentaenoic acid (20:5n-3, EPA) into TAGs were found in the marine microalgae Nannochloropsis oculata (Eustigmatophyceae), Phaeodactylum tricornutum and Thalassiosira pseudonana (Bacillariophyceae), and the Haptophyte Pavlova lutheri. Differences were not only observed between species but also during the different phases of growth within a species. A much higher percentage of the total cellular EPA was partitioned to TAGs in stationary phase cells of N. oculata compared to P. tricornutum. Although P. tricornutum produces DHA it does not partition it to TAGs. Both T. pseudonana and P. lutheri produce EPA and DHA and partition these to TAGs during the stationary phase of growth. These two species are therefore good candidates for further biochemical and molecular analysis, in order to understand and manipulate the processes that are responsible for the incorporation of LC-PUFAs into storage oils.