Seven zooxanthellae-free species of octocorals (the genera Acanthogorgia, Acabaria, Chironephthya, Echinogorgia, Menella, Ellisella, and Bebryce) and two zooxanthellate octocorals (the genera Paralemnalia and Rumphella) were examined to elucidate their fatty acid (FA) composition. Arachidonic (about 40% of the total FA) and palmitic acids were predominant in all the species studied. Seven furan FA (F-acids) (up to 9.7%) were identified in the azooxanthellate octocorals. The main F-acids were 14,17-epoxy-15-methyldocosa-14,16-dienoic and 14,17-epoxy-15,16-dimethyldocosa-14,16-dienoic acids. In all specimens of Bebryce studeri, C(25-28) demospongic FA (about 20%) were identified. These FA reflect the presence of a symbiotic sponge in B. studeri and can be used as the specific markers for other corals. A significant difference (P < 0.01) between azooxanthellate and zooxanthellate corals was found for odd-chain and methyl-branched saturated FA, 18:1n-7, and 7-Me-16:1n-10; that indicated the presence of an advanced bacterial community in azooxanthellate corals. The zooxanthellate species were distinguished by significant amounts of 18:3n-6, 18:4n-3, and 16:2n-7 acids, which are proposed as the markers of zooxanthellae in soft corals. Contrary to the normal level of 24:5n-6 (9.4%) and 22:4n-6 (0.6%), unexpected low concentrations of 24:5n-6 (0.4%) accompanied by a high content of 22:4n-6 (up to 11.9%) were detected in some specimens. The presence of an unknown factor in octocorals, specific for n-6 PUFA, which inhibited elongation of 22:4n-6 to 24:4n-6, is conjectured.