The present study investigates the detailed lipid classes and their fatty acid (FA) compositions from two parasitic copepods Lernaeocera lusci and Peroderma cylindricum and their respective fish host species Merluccius merluccius and Sardina pilchardus. The lipid classes, including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylinositol (PI), triacylglycerol (TAG), wax ester/cholesterol ester (WE/CE), mono-diacylglycerol (MDG), and free fatty acids (FFA) were separated by thin layer chromatography. The results revealed that TAG and PC were the major lipid classes in parasites; while WE/CE and PS were the most abundant in hosts. As for FA composition, C16:0, C18:0, C18:1n-9, C20:5n-3, and C22:6n-3 were recurrently found to be dominant in all lipid classes of the different organisms studied. However, some differences concerning the abundance and the distribution of several FAs were observed. Overall, the obtained results highlighted that despite the quite strong trophic connection between the parasites and their respective hosts, the parasites could be distinguished by specific lipid profiles.