The fan mussel Pinna nobilis is a rapidly growing suspension-feeding bivalve endemic to the Mediterranean Sea and usually inhabits seagrass meadows. This endangered bivalve assimilates carbon and nitrogen isotopic ratios in tissues from its food sources. The δ¹³C and δ¹⁵N signatures were used to demonstrate isotopic variation among three tissues (digestive gland, gills and muscle) and (for digestive gland and gills) between summer and winter. Isotopic values were in the order: gills ≈ muscle > digestive gland. The mean values of the isotopic signal for δ¹³C were –20.41 ± 0.12‰, –19.78 ± 0.07‰ and –19.30 ± 0.5‰ and for δ¹⁵N were 2.84 ± 0.11‰, 4.05 ± 0.14‰ and 3.51 ± 0.15‰ for the tissues digestive gland, gills and muscle, respectively. Seasonal variations (summer–winter) were found in the isotopic signals (δ¹³C and δ¹⁵N) for digestive gland and gills of fan mussel. As a result, this study suggests muscle as the appropriate tissue for future trophic studies and indicates that isotopic signals should be compared in the same season. These δ¹³C and δ¹⁵N values are among the first available for P. nobilis and contribute to the library of δ values for marine invertebrates.