A feeding factorial experiment was conducted, in which Artemia was enriched with two organic selenium (Se) concentrations (0, 12 mg/L) and three highly unsaturated fatty acids (HUFA) levels (0, 0.3 and 0.6 g/L) to produce six dietary treatments, labelled as H0, H03, H06, H0S; H03S and H06S. The diets were fed to barramundi larvae (11 day after hatching) for 15 days to investigate the combined effects of selenium and HUFA on growth performance, fatty acid composition, skeletal deformities and stress resistance of the larvae. The results showed that enriching Artemia with Se significantly improved the final weight and specific growth rate of the larvae fed non or highest HUFA enrichment levels (P < 0.05). No differences were observed in survival of the larvae fed enriched HUFA diets, but they were significantly higher than those fed unenriched HUFA groups. Dietary Se supplementation significantly increased larval n-3 HUFA and DHA contents. High mortalities were recorded in the larvae fed unenriched HUFA diets, whereas Se supplementation significantly increased the survival of the larvae fed high HUFA level. Fish fed unenriched HUFA Artemia showed significantly higher skeletal deformities than those fed other diets. The results thus indicated the beneficial effects of dietary Se in preventing the reduced growth and stress resistance in the barramundi fed HUFA inclusion diets.