The study was designed to investigate the fatty acid composition in longissimus dorsi (LD) and semimembranosus muscles (SM) and subcutaneous tissue of hybrid (1/4 Lithuanian indigenous wattle, 1/4 wild boar and 1/2 Yorkshire or 1/2 Landrace) pigs. The SM showed a tendency to have lower contents of monounsaturated fatty acids (MUFA) and higher contents of polyunsaturated fatty acids (PUFA) than the LD muscle. No statistically significant differences were observed between the muscles in lipid quality indices, i.e., atherogenic (AI) and thrombogenix (TI) indices and the ratio of hypocholesterolemic and hypercholesterolemic fatty acids (h/H). In the SM, the content of PUFA from Yorkshire-sired hybrids was relatively 47.8% higher, including C18:2n-6, C20:4n-6 and DPA (C22:5n-3) that were higher, respectively, by 44.3%, 86.6% and 51.6% in comparison with those from Landrace-sired hybrids. The gilts had a lower content of MUFA, including C18:1 and C20:1n-9 fatty acids in the LD muscle and tended to have a higher content of PUFA in the SM compared to the barrows. Neither the terminal breed in crossing, nor the gender had any significant effects on the proportions of total saturated, MUFA and PUFA in the subcutaneous tissue.