Five experimental diets containing different lipid sources, fish oil (D1), soybean lecithin (D2), corn oil (D3), canola oil (D4) and olive oil (D5), were evaluated in Atractosteus tropicus larvae for the relative gene expression of the enzymes fatty acid synthase (fas), acetyl‐CoA carboxylase 1 (acc1) and carnitine palmitoyltransferase 1C (cpt1c), in addition to their effects on larval growth, survival and cannibalism during a 30‐day feeding trial. Higher growth and survival were obtained in treatments D1 and D2, and lower performance in diets D3, D4 and D5. The highest levels of expression of fas and acc1 occurred in larvae fed with D1, which contained high amounts of n‐3 long‐chain polyunsaturated fatty acids (LC‐PUFA), mainly DHA and EPA FA are regulators of lipogenesis. The higher cpt1c expression in plant‐based diets is attributed to the fact that these diets are rich in α‐linolenic acid (ALA) and low DHA, EPA and ARA levels that favour ß‐oxidation. In conclusion, the diets with fish oil (D1) and soybean lecithin (D2) were the best treatments for larval growth, survival and cannibalism and thus appear to meet both lipid and energy requirements of A. tropicus larvae, meanwhile the use of vegetable oils influences the expression of intermediary lipogenic genes.