In this study we aimed to characterize the molecular mechanism of toxicity in a bivalve species at environmentally realistic concentrations. To reach such a goal, Mediterranean mussels Mytilus galloprovincialis, representing an ecologically and economically important species, has been exposed for 21 days to three different environmentally realistic glyphosate concentrations and digestive gland transcriptional changes have been investigated using RNA-seq on an Illumina 4000 platform.