Highlights Diversity of SNPs of meat quality-related genes in commercial and creole pigs in the north-west of Argentina. Prevalence of deleterious alleles of the RYR1 and RN gene in creole and commercial pig populations. RYR1, RN, CAST, and SOX6 show high level of polymorphism and heterozygosity. Pig genotypes are an important source of basic variability potentially affecting processed meat products as well as fresh meat.