Persistent chemicals and new emerging pollutants are continuously found in marine waters and biota. Out of these, polycyclic aromatic hydrocarbons (PAHs) are carcinogens or probable carcinogens and capable of long term harmful effects in vertebrates. They are common marine pollutants due to shipping activity and oil spill accidents. Also, organochlorine pesticides (OCs) constitute a family of persistent, lipid-soluble compounds that include industrial chemicals. The Mediterranean Sea is an ecosystem directly affected by a variety of anthropogenic activities including industry, municipal, touristic, commercial and agricultural activities. The Mediterranean mussel is Mytilus galloprovincialis, which is wide distribution and has common use as sea food. These marine organisms are filter feeders and were selected because they have only a limited ability to metabolize organic pollutants especially PAHs and are therefore often used to monitor PAHs contamination in the marine environment. The presented work was implemented in the frames of a bilateral funded project (GSRT) between Greece and Turkey entitled "Pollution monitoring of the Northern Aegean coast by use of transplanted mussels: determination of priority pollutants and their levels and development of suitable biomarkers". In this regard a gas chromatographic tandem mass spectrometric method (GC-MS/MS) was developed and validated to monitor 34 compounds (16 EPA priority PAHs and 18 OCs) whose sample preparation steps were based on previously described QuEChERS procedure. Analyses of Turkish samples of 2011 have shown the occurrence of 7 pollutants (5 PAHs, 2 OCs) in a total of 11 samples. Hence pollutants with high bioconcentration potential were detected in mussels' samples a fact which has to be considered for risk assessment purposes. Monitoring and analyses of first batch of Greek samples and second batch of Turkish samples are currently underway.