For the first time, Anisakidae larvae in commercially caught fish from the southwestern Ionian Sea off the Albanian coast were identified using molecular techniques. Atlantic horse mackerel (Trachurus trachurus) from the Vlora district were examined for parasitic infections. Enzymatic digestion revealed the presence of Anisakis spp. larvae, which were subsequently analysed at ISS Rome by multiplex PCR and PCR-RFLP. Molecular results confirmed the larvae as Anisakis pegreffii. This study provides the first molecular confirmation of Anisakis species in Albanian waters. The detection of Anisakis larvae highlights potential risks for seafood safety and public health, underlining the importance of regular monitoring and risk assessment in the region.