Context Owing to the multiple functions of lipids and fatty acids in organisms, lipid composition can be used as an environmental biomarker of the health status of sentinel organisms in monitoring studies of aquatic ecosystems. Aims To study the lipid profile of the mussel Mytilus galloprovincialis from the Black Sea and to identify lipid compounds as environmental biomarkers. Methods Lipid and fatty acid compositions in the gills and digestive glands of mussels were analysed by chromatography. Key results Membrane-state fatty acid indices in phospholipids were quite stable in all the mussels examined. The fatty acid composition of triacylglycerols is primarily an indicator of the food source for mussels. The selective retention of arachidonic acid as well as the accumulation of non-methylene-interrupted fatty acids in mussels are assumed to be biomarkers of environmental stress. Conclusions The presence of regulatory mechanisms ensuring the stability of the membrane structure was confirmed in all studied mussels. Implications The content of minor phospholipid fractions (namely, phosphatidylinositol and sphingomyelin) and the distribution of some fatty acids and their indices among lipid classes in the gills and digestive glands of M. galloprovincialis can be used in the assessment of the health status of sentinel organisms.