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This study aimed to evaluate the effect of different factors (season, gender, location, total lipid, weight and length) on the fatty acid composition and nutritional quality of Cyprinion macrostomus. The results were evaluated through PERMANOVA, principal coordinates (PCO), and cluster analysis for similarity ranges. An analysis of similarity (ANOSIM) was performed on the distance matrix using multiple permutations within a significant fixed effect (p < 0.05). C18:1ω9, EPA and DHA were the most important fatty acids which had an effect on the nutritional quality in all the factor groups. Total lipid amount, season and length factors were the most influential on the fatty acid compositions of C. macrostomus. Summer and Spring were the best the periods for the good nutritional quality of C. macrostomus in terms of AI (Atherogenicity index), TI (Thrombogenicity index) and h/H (Σhypocholesterolemic/Σhypercholesterolemic fatty acid index). In addition, station, gender and weight had no effect on nutritional quality. The study indicated that C. macrostomus is a potential fish meat for human nutrition with high nutritional value in terms of fatty acid composition.