Paraffin waxes are widely recognized as emerging marine pollutants, even their classification by the recent monitoring programs and the knowledge of their occurrence, and sources of contamination in marine ecosystems are poorly defined and reported. Wax presence and distribution have been evaluated in different environmental compartments in the Pelagos Sanctuary (Mediterranean Sea) floating on the sea surface and stranded on beaches, focussing on their characterization, accumulation areas and pollution inputs. More than 2,500 yellow paraffin residues were detected and analysed in the study area showing a prevailing dimension smaller than 5 mm. The Genoa Canyon and the waters facing Gorgona Island resulted in the more polluted areas representing two distinct hotspots of wax accumulation potentially related to the high density of tanker vessels sailing to and from the harbour of Genova and Livorno. Higher concentrations of beached particles were found along the Tuscan coast (11 items/100 m) and on Pianosa Island (110 items/m2). This study gives valuable insights into paraffin wax pollution in the Pelagos Sanctuary, emphasizing the need for harmonized monitoring and detection methods to elucidate the potential impacts on marine organisms. Moreover, mitigating actions are crucial to prevent and curb the waxes pollution of marine ecosystems.