Delta(6)-Desaturase (linoleoyl-CoA desaturase, EC 1.14.19.3) is the rate-limiting enzyme in the biosynthetic pathway of highly unsaturated fatty acid (HUFA). In this report, a Delta6 desaturase-like cDNA was cloned, and the relation of HUFA biosynthetic activity in liver with ambient salinity as well as dietary fatty acids was investigated in the euryhaline teleost Siganus canaliculatus. After the juveniles were fed four formulated diets (D1-D4) with different essential fatty acid composition (D1 with 23.49% HUFA, D2-D4 were HUFA-free, linoleic and alpha-linolenic acids account for 21.1% and 0.38%, 13.99% and 11.64%, 18.31% and 5.82% of the total fatty acids, respectively) for nine weeks, the growth performance showed no difference among groups in brackish water (10 ppt) or seawater (32 ppt) (P>0.05). Comparing liver fatty acids with fish fed D1, the content of arachidonic acid in fish fed D2 or D4 was significantly higher in 10 ppt (P<0.05), but showed no difference in 32 ppt; the contents of eicosapentaenoic (EPA), docosapentaenoic (DPA) and docosahexaenoic (DHA) acids in 10 ppt, as well as EPA in 32 ppt in fish fed D3 showed no difference, whereas those of DPA and DHA were significantly lower in 32 ppt (P<0.05). These data suggest that S. canaliculatus may convert linoleic and alpha-linolenic acids into HUFA and such a capacity was stronger in low salinity than that in high salinity. Consistent with this, the liver levels of Delta6 desaturase mRNA in fish fed D2-D4 were generally higher than in fish fed D1 in both salinities, and the total expression level in 10 ppt was about 1.56 times of that in 32 ppt, suggesting that transcriptional control of Delta6 desaturase is involved in such a HUFA biosynthesis. To our knowledge, this is the first report showing the relation of HUFA biosynthetic activity with ambient salinity in a euryhaline fish.