The genus Thunnus comprises many species, some of higher quality and commercial value for their excellent organoleptic features, while others of lower quality and value. Consequently, these species are subjected to frequent fraudulent substitution. Increasing trade in fillet and minced fish makes the identification of external anatomical and morphological features of fish impossible. Proteomics was used for the identification of three Thunnus species. Muscle extracts were evaluated by both mono- and two-dimensional electrophoresis and mass spectrometric techniques. Preliminary results demonstrate that the tested species displays a high degree of polymorphism, making possible an accurate identification.