Sea lice are copepod ectoparasites that constitute a major barrier to the sustainability and economic viability of marine finfish aquaculture operations worldwide. In particular, the salmon louse, Lepeophtheirus salmonis, poses a considerable problem for salmoniculture in the northern hemisphere. The free-swimming nauplii and infective copepodids of L. salmonis are lecithotrophic, subsisting principally on maternally-derived lipid reserves. However, the lipids and fatty acids of sea lice have been sparsely studied and therefore the present project aimed to investigate the lipid and fatty acid composition of sea lice of the genus Lepeophtheirus obtained from a variety of fish hosts. Total lipid was extracted from eggs and adult female L. salmonis obtained from both wild and farmed Atlantic salmon (Salmo salar L.) sampled at two time points, in the mid 1990s and in 2009. In addition, L. salmonis from wild sea trout (Salmo trutta L.) and L. hippoglossi from wild Atlantic halibut (Hippoglossus hippoglossus L.) were sampled and analyzed. The lipids of both females and egg strings of Lepeophtheirus were characterized by triacylglycerol (TAG) as the major neutral (storage) lipid with phosphatidylcholine and phosphatidylethanolamine as the major polar (membrane) lipids. The major fatty acids were 22:6n-3 (DHA), 18:1n-9 and 16:0, with lesser amounts of 20:5n-3, 22:5n-3 and 18:0. L. salmonis sourced from farmed salmon was characterized by higher levels of 18:2n-6 and 18:3n-3 than lice from wild salmon. Egg strings had higher levels of TAG and lower DHA compared to females, whereas L. hippoglossi had lower levels of TAG and higher DHA than L. salmonis. The results demonstrate that the fatty acid compositions of lice obtained from wild and farmed salmon differ and that changes to the lipid and fatty acid composition of feeds for farmed salmon influence the louse compositions.