We combined the use of pigments, fatty acids and sterols as biomarkers of the seasonal variation in food sources of the great scallop Pecten maximus. From March to October 2011, on a biweekly to twice-weekly basis, scallops and seawater from the water column and the water-sediment interface were collected in the Bay of Brest (Brittany, France). Pigment compositions in the seawater and in the stomach and rectum content of the scallops were analyzed by HPLC. Fatty acids and sterols from digestive gland (DG) tissue were analyzed by gas chromatography. Potential relationships between the temporal proportion of each marker in the environment and in the digestive tract were tested using multivariate analysis. Proportions of diatoms and Dinophyceae biomarkers alternated in the digestive tract of P. maximus. This switch of feeding was confirmed by the polar lipid composition of the DG. Peridinin, characterizing Dinophyceae, occurred in high proportions in the digestive tract compared to the low ambient concentration, suggesting a selection of this microalgae group by the scallop. Chlorophyceae and green macroalgae tracers were found in low proportions, suggesting they were not actually ingested. Markers of Prymnesiophyceae were also observed at significant levels. Cyanobacteria tracers showed that this microalgae class was not ingested by the scallops during monitoring but may be of higher importance during winter. Switching from one food source to another as well as selectivity in feeding are discussed relative to the season.