Skin and gill parasites found in juvenile Atlantic bluefin tuna (Thunnus thynnus) caught in the Bay of Biscay, northeast Atlantic, were examined with the aim of finding biological tags. The degree of infection of different microhabitats was analyzed and the annual prevalence by species of parasite obtained. Of the specimens examined, 98% had parasites, and the gills were by far the most infected microhabitat, followed by the skin and the pectoral fin. Within the gill cavity, parasites were most commonly found in the afferent margins of the primary lamellae. Three species of Copepoda were identified, two species of Monogenea, and eleven Digenea. Thus, ten species (Digenea: Didymozoidae) and a new host record for Copiatestes thyrsitae (Digenea: Syncoeliidae) were recorded in Thunnusthynnus. The suitability of the different external parasites found is discussed and gill didymozoids are put forward as useful biological tags. Confusing taxonomy within this digenean family makes species identification of the different morphotypes difficult. However, their habitat specificity in hosts can be a good tool to differentiate morphotypes and characterise host individuals.