The main objective of this study was to analyse the differences in morphometric characteristics among specimens of Atlantic juvenile bluefin tuna Thunnus thynnus [12.2-46.5 cm fork length (FL)] and juvenile little tuna Euthynnus alletteratus (14.1-26.4 cm FL). A total of 353 bluefin tuna (young of the year) and 288 little tuna (young of the year) were collected from the commercial hand line fisheries in the eastern Mediterranean Sea between July and October of 2011-2013 with three round-bent hook sizes (numbers 10, 12 and 14; Mustad 2315S). By using univariate and multivariate analysis, 11 morphometric characters were investigated. ANOVA revealed highly significant differences (P < 0.001) for all morphometric parameters among the two species. The principal component analysis showed that the difference between the species resulted mainly from preanal length (LA), caudal fin hight (CC), snout length (SnL), eye diameter (ED) and postorbital length (PO). The stepwise discriminant analysis revealed that juveniles of the two tuna species were correctly classified, with a percentage of 99.2%. Length of pectoral fin (LP) was the strongest predictor in the discriminant functions.