The lipid composition of five species of green seaweeds ( Chaetomorpha linum , Rhizoclonium riparium , Ulva intestinalis , Ulva lactuca , and Ulva prolifera ) grown in fish pond aquaculture systems was studied. In particular, the overall fatty acid (FA) profile and the FA profile of each main lipid class found in these seaweed species were thoroughly analyzed. It was found that every seaweed had a specific FA profile, whose specificities were rendered more obvious with the study of the FA profile per lipid class. However, between U. lactuca and U. intestinalis , there were only minor differences. Nonetheless, it was possible to identify significant differences between the palmitic acid content in the phospholipid (PL) and glycolipid (GL) classes of each seaweed. A clear distinction between the FA profiles of R. riparium and C. linum , which belong to the Cladophorales order, and those of Ulva genus, Ulvales order, was also determined. Moreover, there were also differences among lipid classes, yielding large contrasts between PLs + GLs and triacylglycerols (TAGs) as well as between monoacylglycerols (MAGs) and free fatty acids (FFAs). This study also found evidence supporting the location of particular FAs in specific TAG positions. FA profiles have the potential to be used as a chemotaxonomic tool in green seaweeds, providing a simple method to check authenticity of seaweed used as food.