Fatty acid profiles of seeds of the mussel Mytilus galloprovincialis originating from two habitats (rocky shore and subtidal) were compared after transfer to the same habitat (subtidal). The objective was to study the initial levels of different fatty acids of metabolic importance and, furthermore, the variability of these fatty acids over the experimental period. The results show that of all fatty acids identified in both seed groups, the polyunsaturated fatty acids (PUFA) is the group with highest percentage. Within this group, the C20:5n-3 and C22:6n-3 fatty acids show the highest levels. Additionally, the mussels of subtidal origin presented higher initial levels than the rocky shore mussels with regard to fatty acids characterised by energetic-type functions, such as the C14:0, C16:0, and the C20:5n-3 fatty acids, among others. Fatty acids characterised by structural-type functions, e.g. C18:0, C22:6n-3 and non-methylene interrupted dienoic (NMID) with 20 and 22 carbons in rocky shore mussels presented higher levels than those of the subtidal mussels. However, it has not been ruled out that aside from influences relating to the functional aspects of the different fatty acids, the initial differences were also associated with the quantitative and qualitative differences of the available food in both habitats. Nevertheless, 22 days into the experiment (in the majority of cases) the initial differences disappear in the different fatty acids with metabolic importance. On the basis of these results, the influence that mussel origin could exercise on the variability of the fatty acid profiles of recognised metabolic importance is discussed.