The objective of this study was to test the potential the alternation of fish oil-and canola oil-based diets offered in a circadian alternating schedule, in gilthead sea bream (Sparus aurata) and European sea bass (Dicentrarchus labrax), two commercially important marine species in Mediterranean aquaculture. The two species were kept separately, juvenile European sea bass and gilthead sea bream were randomly distributed each into 4 triplicate groups at 40 fish per tank (n= 3, N= 12; per species). Two experimental extruded diets differing only in the added dietary lipid sources, either 100% fish oil (FO-D) or 100% canola oil (CO-D), but having the same formulation, were manufactured. The experimental feeding schedules adopted were: CO-D in the first meal with FO-D in the second meal (COam), and FO-D in first meal with CO-D in the second meal (COpm), and two control treatments: a positive control treatment, fed FO-D in both meals (posCT), and a negative control treatment, fed CO-D in both meals (negCT). Test diets were fed twice a day at a 2% body weight per day for 60 days. Gilthead sea bream and European sea bass fed the negCT diets exhibited the poorest performance. The COpm diet worked while the COam diet tended to work equally well as the fish oil diet (posCT) in terms of fish performances and feed efficiency in gilthead sea bream but the posCT diet tended to outperform both COam and COpm diets in European sea bass. Important differences in the whole body nutrient composition were recorded across treatments, as well as in their fatty acid composition. The whole-body contents of n-3 polyunsaturated fatty acids and in particular DHA, but not EPA, were highest with COpm diets followed by COam, posCT and negCT diets, in gilthead sea bream, while were highest with posCT and lowest with negCT diets with a similar response with COam and CO-pm diets in European sea bass. This study showed that the daily alternation of fish oil-and canola oilbased diets in comparison to the continuous feeding with either fish oil-or canola oil-based diets can enhance growth performance and feed intake and can promote EPA and DHA content in the fatty acid profile of gilthead sea bream. Clear species-specific responses were also observed where the effect of alternate oil feeding on growth performance and feed efficiency as well as on fatty acid profile was less marked in European sea bass. Mixed feeding schedules, based on at hoc circadian patterns, may be instrumental to optimise fish oil use in aquafeeds, maintain the targeted n-3 fatty acids in fish tissues and ultimately support the further growth of an environmental sustainable and economically viable aquaculture industry.