<p>This study examined the genotype distribution of the stearoyl-coenzyme A desaturase (SCD) and fatty acid synthase (FASN) gene loci and their association with milk fatty acid composition in Holstein cows. The SCD and FASN gene loci genotype distribution was found in Hardy-Weinberg Equilibrium. The SCD gene locus showed a genotype distribution of 122, 28, and 20 bp (TT), 122, 75, 47, 28, and 20 bp (TC), and 75, 47, 28, and 20 bp (CC) with frequencies of 0.21, 0.44, and 0.35, respectively. Meanwhile, T and C allele frequencies were 0.43 and 0.57, respectively. For the FASN gene locus, the frequencies of genotypes 273, 217, 167, and 101 bp (AA), 440, 273, 217, 167, and 101 bp (AG), and 440, 217, and 101 bp (GG) were 0.15, 0.35, and 0.50, respectively, with allele frequencies of 0.33 for A and 0.67 for G. Significant relationships were observed between the SCD gene polymorphism and the fatty acids C4:0, C11:0, C18:1 trans6, C18:3n3, and C20:2, with the highest averages recorded in the TT and TC genotypes. The FASN gene polymorphism was associated with saturated fatty acid, monounsaturated fatty acid, and polyunsaturated fatty acid, notably C14:0, C18:1 trans9, C18 trans11, C24:1 n9, C18:2n6, C18:3n3, and C22:6 n3, with prominent prevalence in the AA, GG, and AG genotypes. These findings underscore the potential significance of these gene polymorphisms in influencing fatty acid profiles, and they might be potential markers for modifying fatty acid composition.</p>