Two bacteria-bearing mussels, Bathymodiolus brevior and B. elongatus, collected at five deep-sea hydrothermal sites from Lau and Fiji back arc basins (south-west Pacific), were analysed for polar and neutral lipids using gas-liquid chromatography mass spectroscopy (GLC-MS). The respective fatty acid distributions found in gills and mantles were compared to data from a Mediterranean littoral filter-feeding mussel, Mytilus galloprovincialis. The main characteristic common to the gills of the two vent mussels was the high level of (n-7) monounsaturated phospholipid fatty acids, which are supposed to originate from sulphur-oxidizing symbionts. Using palmitoleic, 16:1 (n-7), and vaccenic, 18:1 (n-7), phospholipid fatty acids as bacterial markers, endobacterial biomass was estimated to account for 2–10% of the vent mussel gill volume. Vent mussel tissues were poor in plant-derived polyunsaturated fatty acids, indicating the limited importance of the photosynthesis based material in the metabolism of these hydrothermal vent bivalves. It is suggested that some compounds, such as nonmethylene-interrupted dienoic fatty acids and specific trienoic fatty acids originating from elongation and desaturation of oleic and palmitoleic acids, respectively, were synthesized in order to substitute exogenous plant-derived polyunsaturated fatty acids considered as essential in marine invertebrates. The high level of neutral lipids in vent mussel gills suggests that these compounds are used as a major energy storage material. The neutral lipid/phospholipid ratio in gills emphasized the preponderance of the endosymbionts in vent mussel nutrition. Using this ratio as an index of the physiological state, the symbiosis patterns in different hydrothermal fields were compared.