Organ-specific modifications and assimilation of trophic lipids, primarily of their fatty acids, were shown in the study of compensatory lipid and fatty acid composition changes in blue mussels Mytilus edulis L. as a result of acclimation to laboratory conditions using commercial plankton-based food. It was found that phospholipid fatty acid composition of mussel gills does not depend on food source, while triacylglycerol fatty acid composition exactly reflects the trophic fatty acid profile. Significant changes in the content of the main lipid fractions and their fatty acids in digestive glands of acclimated mussels were apparently caused by absence of essential phytoplankton polyene n-3 fatty acids in the feed. However, increased concentration of triacylglycerols enriched with short-chain saturated fatty acids, α-linolenic and vaccenic acids in the commercial food promoted the accumulation of these lipids in investigated mussel’s tissues.