The present study evaluated fatty acid (FA) metabolism in juvenile gilthead sea bream (Sparus aurata, 60.4 +/- 4.9 g) fed diets with camelina seed oil and chia oil which totally (CSO and CO diets, respectively) or 60% (60CSO and 60CO diets, respectively) replaced fish oil (FO diet) for 90 days. Analysis of the expression of genes was carried out to determine the effects of the diets on some of the major genes involved in fatty acid metabolism in fish. Good growth performance was recorded in all fish although lower growth (P < .05) was recorded in CSO fed fish. Body FA compostions were modified reflecting dietary FAs. Although alpha-linolenic acid (ALA, 18:3n-3) was the preferential substrate for beta-oxidation, feeding CSO- and CO-based diets did not result in increased beta-oxidation. Increased in vivo elongase and desaturase (Delta-6 and Delta-9) activities were recorded in fish fed fish oil-devoid diets, which resulted in the appearance of products associated with elongase and desaturase activities in fish. The expression of genes involved in polyunsaturated FA (PUFA) metabolism was higher in fish fed vegetable oil-based diets, corroborating the results of the whole body FA balance method. However, apparent in vivo Delta-5 desaturase activity could not be determined when the whole body FA balance method was applied. With diets limited in supply of highly unsaturated FA (HUFA), the appearance and accumulation of products from the elongation and desaturation of dietary ALA and LA signify attempts by juvenile gilthead sea bream to alleviate EFA deficiencies in their diets. However, the de novo synthesis was not enough to alleviate the EFA deficiencies.