Samples of Mytilus galloprovincialis were examined to investigate the levels of polybrominated diphenyl ethers (PBDEs) in the Apulia's marine environment, a region in the South of Italy. The levels of nine PBDE congeners were measured in 40 mussel samples taken from the aquaculture farms in the South of Adriatic Sea and North Ionian Sea along the Apulia coast. While accelerated solvent extraction (ASE) was the extraction technique adopted using acetone/n-hexane (1:1, v/v), the content of PBDEs was evaluated by using gas chromatography coupled with high-resolution mass spectrometry (GC–HRMS) via electron ionization (EI) in the multiple ion monitoring (MIM) mode (two ions for each compound). The 13C mass-labeled compounds were used to establish the levels of PBDEs in M. galloprovincialis samples. The total concentration of PBDEs (ΣPBDEs) ranged from 0.2 to 6.9 ng/g dry mass, with the highest concentrations found around coastal areas of Salento. With regard to the composition of PBDE congeners, BDE-47, BDE-99 and BDE-100 were the predominant congeners in most of the samples. The present study is the first to report levels of PBDEs occurring in aquatic organisms living in aquaculture farms of Apulia region. Copyright © 2010 John Wiley & Sons, Ltd.