In recent years, the presence of organic pollutants (OPs) in biota samples, especially in species which are intended for human consumption, has generated major concern. Thus, legislation on presence and levels has been created and/or updated in order to achieve safe food products for consumers. During the years 2020 and 2022 in the frame of the project "Contaminant levels in species of commercial interest captured in the Portuguese Maritime Area - CEIC", different species of fish and molluscs were collected in 4 main areas of the Portuguese coast. Samples were processed by matrix solid-phase dispersion (MSPD) and injected into gas and liquid chromatographic systems coupled to high resolution mass spectrometry analysers. A total of 82 OPs were identified using liquid chromatography (LC), most being pharmaceuticals, 56 OPs were identified by gas chromatography (GC) using a high-resolution mass spectra library. In addition, 38 chlorine/bromine-containing compounds were tentatively identified using the low resolution NIST 2017 database, most of which are used as industrial chemicals. Cluster analysis of samples revealed grouping according to the type of analysed tissue, sampling area and campaign. For the per- and polyfluoroalkyl substances (PFAS) detected, a quantitative methodology was applied to evaluate concentration levels. Several fish muscle and bivalve mollusc samples exhibited PFAS concentrations that exceeded the permitted levels established by current regulations, with perfluorooctanoic acid (PFOA) showing particularly elevated levels in the analysed samples. In conclusion, the study highlights the widespread occurrence of organic pollutants, particularly PFAS, in commercial marine species along the Portuguese coast, underscoring the urgent need for continued monitoring.