The use of tributyltin (TBT) as a biocide in antifouling paints leads to a ruinous input of this contaminant in the aquatic environment. Human exposure to TBT mainly occurs through ingestion of contaminated seafood such as filter-feeding mollusks. Tributyltin is known to act as a membrane-active toxicant on several targets, but especially on the mitochondria, and by several mechanisms. The effects of tributyltin on fatty acid composition, on Mg-adenosine triphosphatase (ATPase) activities, and on the membrane physical state were investigated in gill mitochondrial membranes from cultivated mussels Mytilus galloprovincialis exposed to 0.5 µg/L and 1.0 µg/L TBT and unexposed for 120 h. The higher TBT exposure dose induced a decrease in the total and n-3 polyunsaturated fatty acids (PUFAs), especially 22:6 n-3, and an activation of the oligomycin-sensitive Mg-ATPase. Both TBT concentrations decreased mitochondrial membrane polarity detected by Laurdan steady-state fluorescence spectroscopy. These findings may help cast light on the multiple modes of action of this toxicant.