The efficiency of the green extraction methods ultrasound‐assisted extraction (UAE) and microwave‐assisted extraction (MAE), and conventional methods (Soxhlet and Bligh and Dyer), on lipid content and fatty acid profiles of six fish species (Mullus barbatus, red mullet; Upeneus moluccensis, goldband goatfish; Mullus surmuletus, surmullet; Anguilla anguilla, European eel; Pagellus erythrinus, common pandora, and Saurida undosquamis, brushtooth lizardfish) are evaluated. The results of lipid content of fish species show that the Bligh and Dyer method and UAE in general are more efficient than other methods. There are statistical differences in the fatty acid composition of fish oil by four extraction methods (p < 0.05). Saturated (SFA), monounsaturated (MUFA), and polyunsaturated fatty acid (PUFA) contents of fish species range from 29.51 mg 100 g−1 fish (Soxhlet)–1400 mg 100 g−1 (UAE), 15.52 mg 100 g−1 (UAE)–2237.18 mg 100 g−1 (Bligh and Dyer), and 14.36% (Soxhlet)–646 mg 100 g−1 (Bligh and Dyer), respectively. Generally, Bligh and Dyer give the higher values in surmullet, red mullett, and common pandora in terms of SFA, MUFA, PUFA, and the dominant fatty acids (C16:0, C18:0, C16:1, C18:1n9, C18:1n7, C22:1n9, EPA, DHA), whereas MAE and UAE methods give better results in goldband goldfish and European eel, respectively. Thus, extraction methods affect the lipid yield and fatty acid profiles of extracted oil of different fish species. Practical Application: Total lipid content of seafood is an important parameter used in biochemical, physiological, and nutritional studies. Thus, reliable methods for the quantitative extraction of lipids from this type of food are of critical importance. The effects of green and conventional extraction methods on lipid yield and fatty acid profiles of fish species are compared in order to determine the most effective method for extracting lipid with high yield and high content of PUFA, especially EPA and DHA. The effects of green and conventional extraction methods on lipid yield and fatty acid profiles of fish species are evaluated. The extraction methods affect the lipid yield and fatty acid profiles of extracted oil of fish species. The Bligh and Dyer method and UAE in general are more efficient than other methods. In terms of SFA, MUFA, PUFA, EPA, and DHA; Bligh and Dyer gave the higher values in surmullet, redmullet, and common pandora whereas MAE and UAE methods gave better results in goldband goldfish and European eel, respectively.