The composition of fatty acids was studied in the mussels collected in the Mar Grande of Taranto (northern Ionian Sea) during the four seasons. Micro-, nano- and picophytoplankton abundance, biomass and composition have been also evaluated. Fatty acids compositions were investigated for lipid biomarkers to establish the contribution of phytoplankton to the mussel diet. Saturated (SAFA) and monounsaturated fatty acids (MUFA) were the most abundant components, followed by polyunsaturated fatty acids (PUFA). The seasonal variations in the SAFAs, MUFAs and PUFAs were not significantly different during the whole study period (ANOVA, P < 0.05). The most abundant identified FAs were 16:0 (27.51–33.80% of total FAs), 14:1 (3.35–9.91% of total FAs), 18:1n9 (2.92–8.87%), 16:1 n7 (4.53– 7.61%) and 24:1n9 (0.43–8.84%). The most important PUFAs were 22:2 (2.35–3.48% of total FAs) and also 18:2n-6 (1.66–2.61%). PUFAs were characterized by low percentages of n3 and n6 FAs. Analysis of specific FA markers for diatoms (16:1n7, 20:5n3), phytoflagellates and dinoflagellates (16:0, 18:4n3) showed a negligible contribution of phytoplankton to the mussel diet.