Two species of euphausiids (Thysanoessa macrura Sars and Euphausia vallentini Stebbing) from the Southern Indian Ocean were analysed for their lipid content, fatty acid and fatty alcohol composition, in relation to developmental stage (T.m) and sex (E.v). Lipid composition showed wax esters and triacylglycerols as main neutral lipids for T. macrura and E. vallentini respectively. Allometric relationships between lipid class and total lipids indicated that changes in total lipids were size dependent and mainly related to wax esters in T. macrura and polar lipids (both phosphatidylcholine or PC and phosphatidylethanolamine or PE) in E. vallentini. No difference in lipid composition could be shown for male and female E. vallentini, while sampling location, developmental stage and sex were significantly influential in T. macrura. In this latter species wax esters displayed relatively similar fatty acid and alcohol composition in both juvenile and female stages, whereas a striking difference could be seen between females and juveniles in terms of polar lipids with a very low PE content in females. Male and female E. vallentini showed little differences in fatty acid structure with the exception of PC in females, which were low in 22:6n-3. The trophic status of these two species was established using multivariate discriminant analysis, which indicated for E. vallentini a degree of omnivory similar to E. superba, while these T. macrura appeared more omnivorous than individuals collected in other areas of the Southern Ocean. Clustering of polar lipid composition suggested a link between differences in PC fatty acid and the post-spawn stage of the female of E. vallentini collected. The same probably applies for the changes in PE recorded for T. macrura females.