The lipid, FA, and sterol composition of the New Zealand green lipped mussel (NZGLM, Perna canaliculus) and of the Tasmanian blue mussel (TBM, Mytilus edulis) were compared using TLC-FID and GC-MS. The respective mussel species were obtained from three different sites in both New Zealand (NZ) and Tasmania. Lipid class distribution of both mussel species was characterized by a high proportion of phospholipid (PL, 57-79%) and TG (10-25%), FFA (7-12%), and sterols (ST, 12-18%). The NZGLM had higher proportions of TG, FFA, and ST (P < 0.01), whereas the TBM had a higher proportion of PL (P < 0.01). There were higher proportions of total PUFA, saturated FA, n-3 FA, and hydroxy and nonmethyleneinterrupted FA (P < 0.05) in the TBM compared with the NZGLM. The major FA in the NZGLM were 16:0 (15-17%), 20:5n-3 (14-20%), and 22:6n-3 (11-17%). The same FA dominated lipids in the TBM, although there were significantly higher proportions of 16:0 (P = 0.000) and 22:6 n-3 (P = 0.003) and lower proportions of 20:5n-3 (P = 0.0072) in the TBM. A novel PUFA, 28:8n-3, was detected in both mussels with higher amounts in the TBM, which probably reflects a greater dietary contribution of dinoflagellates for this species. Cholesterol was the dominant sterol in both mussels. Other major sterols included brassicasterol, 22-methylcholesterol, trans-22-dehydrocholesterol, and desmosterol. There were significant differences (P < 0.05) between the NZGLM and TBM for 12 of the 20 sterols measured. Six sterols showed significant site differences for the NZGLM, and 10 for the TBM. The differences in the FA and sterol composition between the two species may be due to the diet of the NZGLM being more diatom-derived and the diet of the TBM having a greater dinoflagellate component.