The gills of 31 skipjack tuna Katsuwonus pelamis (L.) caught in the Alboran Sea (western Mediterranean Sea) were examined for metazoan parasites, and the gills of 4 specimens from the Balearic Sea (also western Mediterranean Sea) were analysed for comparative purposes. Nine -species of parasites were found, including 8 didymozoid trematodes (Atalostrophion cf. bio-varium, Didymocylindrus filiformis, Didymocylindrus simplex, Didymocystis reniformis, Didymoproblema fusiforme, Didymozoon longicolle, Koellikeria sp. and Lobatozoum multisacculatum) and 1 caligid copepod (Caligus bonito). Koellikeria sp. and L. multisacculatum were not recorded in the Balearic Sea. Most of the parasites (79.2% of all specimens) were didymozoids. Didymozoon longicolle was the dominant species; A. cf. biovarium, D. simplex, D. fusiforme and L. multisacculatum are reported from the Mediterranean Sea for the first time. No correlation was found between the intensity of infection of any parasite species and host size or sex. Most of the parasites, particularly didymozoids, showed a high site-specificity. Significant differences were found between the parasite assemblages of K. pelamis from the Alboran Sea and from the Atlantic Ocean. D. fusiforme, D. longicolle and L. multisacculatum are suggested as potential tags to follow skipjack tuna migrations between the Atlantic Ocean and Mediterranean Sea.