The study aimed to evaluate how replacing different proportions of fish oil (FO) with vegetable oils (VO) in the diet of Mediterranean yellowtail, Seriola dumerili (Risso, 1810), affects the fatty acids (FA) signature, i.e.; overall FA profile, in different tissues. A total of 225 Mediterranean yellowtail juveniles (initial live weight: 176 ± 3.62 g) were fed for 109 days with one of three diets: A control diet (FO 100), with FO as the only lipid source, or diets with 75% and 100% of FO replaced with a VO mixture. At the end of the feeding trial, the brains, muscles, livers, and visceral fat were sampled in four fish per tank (12 per treatment), and their fat were extracted and used for FA analysis. The FA signatures of red and white muscle, liver, and visceral fat tissues changed when the dietary FA source changed, whereas FA signatures in the brain were rather robust to such dietary changes. These new insights might help evaluate whether key physiological functions are preserved when fish are fed diets with low FO levels, as well as define the dietary FA requirements of Mediterranean yellowtail to improve the sustainability of the production and welfare of the fish.