The effect of the quality of two microalgal species on select biological and biochemical responses used as indicators of pollution were assessed. Mussels were conditioned for 6 weeks with the diatom Chaetoceros neogracile and the dinoflagellate Heterocapsa triquetra, chosen for being two clearly different types of primary production quality that differ in both biometric and biochemical characteristics. After dietary conditioning, the mussels were exposed to a polycyclic aromatic hydrocarbon, fluoranthene (FLU), for 1 week followed by 1 week of depuration. Results showed higher FLU accumulation in mussels fed on C. neogracile compared to those fed on H. triquetra. Concomitantly, a greater impact of this toxicant was observed in the biomarker responses of mussels fed on C. neogracile. These mussels showed an increase in the percentage of dead hemocytes, an activation of phagocytosis and ROS production of hemocytes after exposure. Some enzymatic activities also increased upon FLU exposure (superoxide dismutase −SOD-, catalase −CAT-, and glutathione reductases −GR-) and after depuration (glutathione-s-transferase −GST-). Results suggest that FLU exposure as well as food quality influence biomarker responses, with higher values of SOD, CAT and GR in non-exposed mussels fed on C. neogracile. In addition, upon exposure to the same FLU concentration, GR response varied according to dietary conditioning, suggesting that diet could act as a confounding factor in biomarker responses to pollution. Consequently, trophic conditions should be considered in marine pollution monitoring programs for a better interpretation of biomarker responses.