Carbon and nitrogen stable isotopes were investigated in separate organs of diploid and sterile triploid Pacific oysters Crassostrea gigas for 13 mo, together with changes in chemical and isotope composition of suspended matter sampled from an intertidal mudflat within Marennes-Oléron Bay, France. Particulate organic matter (POM) was a mixture of pelagic and benthic material with a predominance of neritic phytoplankton in spring, and resuspended microphytobenthos in summer and autumn. A remarkable shift of +30/00 in d13C was reflected in both diploids and triploids from spring to summer, and further temporal differences were observed amongst their tissues. Seasonal changes in POM d15N were also reflected in oyster tissues, with digestive gland and muscle tissues showing the largest and the least variability, respectively. Use of d13C and C:N ratio relationships in separate tissues allowed for an assessment of the influences of trophic condition, seasonal changes, and gametogenic cycle on tissue d13C. Diploid digestive gland d13C matched those of gonads, and differences between diploids and triploids in digestive gland and mantle d13C were less than –10/00 during gametogenesis. The reproductive and rest periods were easily distinguished in these tissues and were characterised by enriched d13C values in summer–autumn compared with spring, which is consistent with POM d13C seasonal changes. A similar trend was observed in muscle, with a preferential incorporation of 13C-enriched carbon during the summer–autumn growing season. However, despite the similar roles of mantle and digestive gland in lipid synthesis in both diploids and triploids, the correlation of d13C with the C:N ratio highlighted the transfer of lipids to gonads in diploids and their differential allocation to growing tissues in sterile triploids.