Quantum dots (QDs) are a class of engineered nanoparticles (ENPs) with several biomedical, industrial and commercial applications. However, their metabolism and detoxification process in aquatic invertebrates and environmental health hazards remain unclear. This study investigate the transcriptional changes of metallothioneins (MTs) isoforms (mt10IIIa and mt20IV) induced by CdTe QDs, in comparison with its dissolved counterpart, in the marine mussel Mytilus galloprovincialis. Mussels were exposed to CdTe QDs and to the same Cd concentration (10 µg Cd L) of dissolved Cd for 14 days and mt transcription levels were measured by real time quantitative PCR (qPCR). Tissue specific mt transcription patterns were observed in mussels exposed to both Cd forms, wherein the gills were a more sensitive organ compared to the digestive gland. No significant changes were observed in mt10IIIa transcription levels in mussels exposed to both Cd forms. In contrast, transcription of mt20IV was tissue and exposure time dependent, with higher mt20IV mRNA levels in mussels exposed to QDs and dissolved Cd when compared to unexposed mussels. Multivariate analysis indicates particle-specific effects after 14 days of exposure and a dual role of MTs in the QD metabolism and in the protection against oxidative stress in mussels exposed to Cd-based ENPs.