The purpose of this study was to investigate the combined effect of the incorporation of vegetable products in diet and temperature on enzymatic pathways for high unsaturated fatty acids (HUFA) desaturation in sea bass larvae. Four replicated groups were fed a low (LH; 0.8% EPA + DHA) or a high (HH; 2.2% EPA + DHA) n-3 HUFA microparticulated diet from mouth opening, six days post-hatching and were reared at 16 or 22 °C. The four experimental conditions (LH16, HH16, LH22 and HH22) were tested for 45 days. At the end of the experiment, body weight, total length and biomass were affected by temperature (P b 0.001), while biomass as well as fresh body weight was also influenced by diet (P b 0.05 and P b 0.001 respectively). This always lead to the same ranking of experimental conditions: HH22 N LH22 N HH16 N LH16. The larval skeletal development was more advanced in 22 °C-groups than in 16 °C-ones (P b 0.001), while it was not affected by diet. Amylase and trypsin pancreatic secretions did not vary between d-25 and d-45, indicating that pancreatic maturation was achieved at d-25. Low temperature combined with low dietary HUFA delayed intestinal maturation (P b 0.001), while low temperature combined with high HUFA diet allowed larvae compensating for the initial intestinal maturation retardation. Lipase gene expression was down-regulated in HH16 group at d-25 (P b 0.05) and in the two 16 °C-groups at d-45 (P b 0.001), while lipase enzymatic activity was similar in all groups. This suggested the presence of a post-transcriptional regulation of this gene. PPAR α and PPAR β were not affected neither by temperature, nor by diet, suggesting that lipid metabolism was not significantly affected by a lowering in dietary n-3 HUFA when isolipidic diets were used. A higher DHA content was found in larvae than in their diets (× 2 for LH; ×1.5 for HH) but the DHA content in PL of d-45 LH larvae was lower than the initial one, which revealed a HUFA deficiency in this group. Delta 6-desaturase (Δ6D) gene expression was significantly up-regulated by HUFA deprived diet (P b 0.05) whatever the temperature was. This was supported by the increase in 18:3n-6 in LH larvae (P b 0.001), which indicated a desaturation from 18:2n-6 by the Δ6D. This study clearly showed that larvae were able to adapt to an n-3 deprived diet by a stimulation of enzymatic pathways for HUFA desaturation, and that this adaptation was not affected by temperature.