The present study aimed to compare the nutritional quality of three fish species (Sparus aurata, Sarpa salpa, and Mullus barbatus) collected from the Bizerte lagoon (South Mediterranean coasts). Proximate composition, fatty acids and nutritional quality indices were determined. Results showed that the nutritional quality of the three fish follows this trend: S. aurata > S. salpa > M. barbatus. S. aurata had significantly higher protein content (16.02 ± 2.01 mg/g ww), glycogen level (1.08 ± 0.16 mg/g ww), and lipid content (8.47 ± 0.96 mg/g ww) which are rich in omega-3 fatty acids (47.34%). The Total Fatty Acid (TFA) profile of S. aurata was dominated by Polyunsaturated Fatty Acids (PUFA) (70.34 ± 0.02%), followed by monounsaturated (MUFA) (20.72 ± 0.04%) and Saturated Fatty Acids (SFA) (9.03 ± 0.01%). The use of different Nutritional Quality Indices (NQI) (n-3/n-6 ratio, PUFA/SFA, EPA+DHA, Atherogenicity (AI) and Thrombogenicity (TI) indices) confirmed that S. aurata is a good source of beneficial Fatty Acids (FA) and an excellent source of nutrients. Overall, the consumption of S. aurata over S. salpa and M. barbatus is highly recommended and can be considered as a healthy food for human consumption.