The changes of the fatty acid (FA) profile of 2 muscles Longissimus dorsi and Biceps femoris from 3 Iberian × Duroc genotypes were studied: GEN1: ♂ Iberian × ♀ Duroc1, GEN2: ♂ Duroc1 × ♀ Iberian; GEN3: ♂ Duroc2 × ♀ Iberian. GEN1 and GEN2 are reciprocal crosses while the difference between GEN2 and GEN3 is the Duroc sire line. The genotype Duroc1 was selected for the production of dry-cured meat products while the genotype Duroc2 was selected for meat production. Longissimus dorsi and Biceps femoris BF from the reciprocal cross showed similar changes in FAs profile after refrigerated storage. However, the Duroc sire line affected the FA profiles of intramuscular fat (IMF) and lipid fractions since some differences were found between GEN2 and GEN3. Meat from GEN3 had the highest level of polyunsaturated fatty acids (PUFA) in IMF and lipid fractions as well as the lowest rate of plasmalogens in polar lipid fraction. After storage, meat from GEN3 showed an increase of long chain PUFA in free fatty acids fraction and the highest increase in the ratio DMA/FA [(dimethylacetals/FAs) × 100] after the refrigerated storage, which was indicative of a higher deterioration of this genotype. Therefore, the crossbreeding of Iberian pigs with Duroc selected genotypes (Duroc2) could affect the changes in the FAs profile of meat under refrigerated storage.