An 8-week trial was performed to evaluate the influence of docosahexaenoic (DHA) and eicosapentaenoic acid (EPA) ratios and temperature on the fatty acid (FA) metabolism and liver morphology of Epinephelus marginatus. A basal diet was manufactured, and DHA (D1:0.5%; D2:0.75%; D3:1%; and D4:1.5%) and EPA (D1:1.0%; D2:0.75%; D3:0.5%; and D4:0%) levels were added. E. marginatus were kept in twelve tanks with a lower temperature (LT, 23.17 ± 0.12 °C) and twelve with a higher temperature (HT, 28.63 ± 0.06 °C). The DHA/EPA ratio did not affect performance, regardless of the temperature, but the animals fed with the D4 diet showed better growth at HT. A higher lipid deposition and a large lipid vacuole area in the hepatocytes at HT were observed, regardless of the diet. Triacylglycerol (TG) in reflected the diet FA profile mainly in the muscle and liver, whereas the phospholipid (PL) was less influenced by the diet. The same DHA content in the TG fraction of muscle (D3 and D4) were observed at LT; however, only the DHA/EPA ratio of D4 could be differentially stored in the TG fraction of muscle (HT). Monounsaturated and polyunsaturated FA increased in the PL of the eyes at HT, whereas saturated FA was reduced in the TG and PL fractions at LT. These results evidence the importance of temperature and a balanced DHA/EPA ratio in the diet of marine fish.