Lophiosilurus alexandri is a carnivorous freshwater fish endemic of São Francisco basin and an endangered species. In this study, we analysed the chemical composition (moisture, protein, ash and lipid), fatty acid profile, and nutritional quality (atherogenic index, thrombogenecity index, ratio between hypocholesterolemic and hypercholesterolemic fatty acids and ω6/ω3 = ratio) of L. alexandri in lotic (river), lentic (hydroelectric dams) environments, under natural fed, and in laboratory controlled conditions fed with commercial diets. Cultured and lentic fish had significantly higher lipid levels (1.5 and 1.9- fold, respectively) than lotic fish. Lentic L. alexandri had significantly higher eicosapentaenoic acid (EPA) levels (4×) than cultured or lotic L. alexandri. Docosahexaenoic acid (DHA) levels were the highest in lentic fish, followed by lotic fish. Lentic fish had greater proportion of fatty acid ω6/ω3 than lotic or cultured fish. The results of this study showed that L. alexandri is a lean fish (1-2% of total lipids) and that the environment has a great influence on the fatty acid profile. These results may be a reference for further studies, primarily as a source of information for conservation L. alexandri through restocking and the development of commercial projects of aquaculture.