This study examined seasonal variations in fatty acid composition of the phospholipid (PL) fraction, triacylglycerol (TAG) fraction, and phospholipid subclass (phosphatidylcholine, PC; phosphatidylinositol, PI; phosphatidylserine, PS; and phosphatidylethanolamine, PE) of muscle tissue of Chondrostoma regium, a freshwater fish inhabiting the Munzur River (Turkey). It was found that the percentages of total monounsaturated fatty acids, myristic acid (C14:0), palmitoleic acid (C16:1n7), oleic acid (C18:1n9), linoleic acid (C18:2n6), and linolenic acid (C18:3n3) were higher in TAG fraction than in the PL fraction. The ratio of total polyunsaturated fatty acids to total saturated fatty acids was 1.44-1.85, the atherogenicity index ranged from 0.36 to 0.46, while the thrombogenicity index was determined to be between 0.17 and 0.21 in total lipids. The n3/n6 ratio ranged from 6.55 to 10.49. The fatty acid levels of the PL and PL subclasses, TAG, and total lipid were influenced by the season. Throughout the year, palmitic acid (C16:0), C18:1n9, eicosapentaenoic acid (C20:5n3, EPA), and docosahexaenoic acid (C22:6n3, DHA) were the most abundant in PC. In PE, the share of n3 fatty acids decreased from November to April, and percentages of EPA, DHA and docosapentaenoic acid (C22:5n3) were high among the n3 fatty acids. The predominant fatty acids in PI were stearic acid (C18:0) and arachidonic acid (C20:4n6), and throughout the year, the share of C18:0 was the highest in November. In the PS fraction, the percentages of C16:1n7 and C18:1n9 were high. In summary, C. regium can be deemed an excellent source of nutritionally valuable lipids and recommended for wider use in the human diet.