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Increasing plastic contamination poses a serious threat to marine organisms. Microplastics (MPs) ingestion can represent a risk for the organism itself and for the ultimate consumer. Through the analysis of the gastrointestinal tract, coupled with stable isotope analysis on the muscle tissue, this study provides insights into the relationship between MPs pollution and ecology in two commercial marine species caught in the Central Tyrrhenian Sea: Aristaeomorpha foliacea and Parapenaeus longirostris. Stable isotope analysis was conducted to determine the trophic position and the trophic niche width. The gastrointestinal tracts were processed, and the resultant MPs were analysed under FT-IR spectroscopy to estimate the occurrence, abundance, and typology of the ingested MPs. The trophic level of the species was similar (P. longirostris TP = 3 ± 0.10 and A. foliacea TP = 3.1 ± 0.08), with an important trophic niche overlap, where 38% and 52% of P. longirostris and A. foliacea has ingested MPs, respectively. Though species-level differences may not be evident regarding MP’s abundance per individual, a high degree of dissimilarity was noted in the typologies of ingested particles. This research provides valuable insights into how MPs enter marine trophic webs, stressing that isotopic niche analysis should be combined with other methods to explain in detail the differences in MPs ingestion.