Glutathione S-transferases (GSTs) are phase II enzymes that facilitate the detoxification of xenobiotics and play important roles in antioxidant defense. We investigated the expression patterns of seven Venerupis philippinarum GSTs ( VpGSTs ) and four Mytilus galloprovincialis GSTs ( MgGSTs ) following exposure to BDE-47. Differential expressions of the seven VpGSTs and four Mg GSTs transcripts were observed, with differences between the hepatopancreas and gills. Among these GSTs, the sigma classes ( VpGSTS1 , VpGSTS2 , VpGSTS3 , MgGST1 , and MgGST3 ) were highly expressed in response to BDE-47 exposure, demonstrating their potential as molecular biomarkers for environmental biomonitoring studies. We obtained the three-dimensional crystal structures of VpGSTs and MgGSTs by homologous modeling. A model to elucidate the binding interactions between the ligands and receptors was defined by molecular docking. Hydrophobic and π were the most often observed interactions between BDE-47 and the GSTs.