The tropical marine sponge Amphimedon terpenensis (family Niphatidae, order Haplosclerida) has previously been shown to possess unusual Lipids, including unusual fatty acids. The biosynthetic origin of these fatty acids is of interest as the sponge supports a significant population of eubacterial and cyanobacterial symbionts. The total fatty acid composition of the sponge was analyzed by gas chromatography/mass spectrometry of the methyl esters. Among the most abundant of the fatty acids in intact tissue were 16:0, 18:0 and 3,7,11,15-tetramethylhexadecanoic (phytanic) acid. In addition, three brominated fatty acids, (5E,9Z)-6-bromo-5,9-tetracosadienoic acid (24:2Br), (5E,9Z)-6 bromo-5,9-pentacosadienoic acid (25:2Br) and (5E,9Z)-6-bromo-5,9-hexacosadienoic acid (26:2Br) were also present. The three brominated fatty acids, together with phytanic acid, were isolated from both ectosomoal (superficial) and choanosomal (internal) regions of the sponge. Analysis of extracts prepared from sponge/symbiont cells, partitioned by density gradient centrifugation on Ficoll, indicated that phytanic acid and the three brominated fatty acids were associated with sponge cells only. Further, a fatty acid methyl ester sample hom intact tissue of A. terpenerrsis was partitioned according to phospholipid class, and the brominated fatty acids were shown to be associated with the phosphatidylserine and phosphatidylethanolamine fractions that are commonly present in marine sponge lipids. The phosphatidylcholine and phosphatidylglycerol fractions were rich in the relatively shorter chain fatty acids (16:0 and 18:0). The association of brominated long-chain fatty acids (LCFA) with sponge cells has been confirmed. The findings allow comment on the use of fatty acid profiles in chemotaxonomy and permit further interpretation of LCPA biosynthetic pathways in sponges. The assignment of the sponge studied, which is currently placed as A. terpenensis, is being supported to some extent, but the species is unusual in having C-25 fatty acids as the major constituent in this group. Other factors, such as season or microenvironmental conditions, may influence observed fatty acid composition which tends to reduce the usefulness of fatty acid profiles as markers in sponge chemotaxonomy.