Two tunicates, Eudistoma sp. and Leptoclinides uniorbis, collected from the tropical waters off Djibouti were investigated for lipids and phospholipid (PL) fatty acids. PL accounted for 38.2% of the total lipids in Eudistoma sp. and for 30.2% in L. uniorbis. PL classes were quantified by normal-phase high-performance liquid chromatography using an evaporative light-scattering detector and revealed essential differences. Eudistoma sp. contained mainly phosphatidylcholine (PC, 70.3% of total PL) and lysophosphatidylcholine (LPC, 11.9%) and was devoid of phosphatidylserine (PS), whereas the major PL of L. uniorbis was PS (59.1%) followed by PC (22.5%) and LPC (8.8%). Gas chromatography-mass spectrometry analyses of fatty acid (FA) derivatives revealed 38 FA in Eudistoma sp., and 35 FA in L. uniorbis, ranged from C(12) to C(24) chain lengths. Polyunsaturated FA accounted for 25.9% in Eudistoma sp. and for 32.3% in L. uniorbis. Interestingly, L. uniorbis contained a high percentage (16.7%) of the 20:5n-3 acid (8.9% in Eudistoma sp.) and the 18:4n-3 acid (4.1%). Significant levels of the 20:4n-6 acid were observed in both organisms (7.8 and 6.0% respectively). Eudistoma sp. contained the rare 20:3n-7 acid (2.3%) only recorded to date in hydrothermal vent animals. The cyclopropane dihydrosterculic acid was identified in both tunicates (0.7 and 0.5% respectively). These latter FA, together with some unusual branched saturated and monounsaturated FA, revealed the occurrence of associated bacteria in the tunicates. Another noticeable feature was a series of eight C(16) to C(18) aldehyde dimethylacetals revealing the presence of plasmalogens at 5.0% in Eudistoma sp. and 14.2% in L. uniorbis. The results of this study were compared with those previously published for other tunicates regarding mainly PL content and FA composition.