Blood flukes of the genus Cardicola Short, 1953 are considered the most potentially pathogenic parasites in bluefin tuna cultures. Morphological study and genetic analyses of the ribosomal internal transcribed spacer ITS-2 and the mitochondrial cytochrome c oxidase 1 (cox1) gene fragments revealed the occurrence of four aporocotylid species (C. forsteri Cribb, Daintith & Munday, 2000, C. orientalis Ogawa, Tanaka, Sugihara & Takami, 2010, C. opisthorchis Ogawa, Ishimaru, Shirakashi, Takami & Grabner, 2011 and Cardicola sp.) in 421 Thunnus thynnus (L.) from the Western Mediterranean (274 fished from the wild and 147 from sea-cages). Cardicola opisthorchis was the most abundant species, with higher prevalence in the cage-reared fish than in those fished in the wild (21 vs 6%, p < 0.05). Adults of three species were recovered: C. forsteri from both gills and heart, C. opisthorchis from heart and C. orientalis from gills. The secondary gill lamellae were profusely infected by eggs of C. orientalis. A fourth species was found in four tunas, based on the molecular analyses of eggs apparently indistinguishable in size and shape from the eggs of C. orientalis. The findings provided evidence that infections with Cardicola spp. differed in relation to locality, host origin (wild vs cage-reared) and site of infection. It is necessary to estimate the possible different pathogenic effects of each species of Cardicola in order to take appropriate control measures.