Background: The genetic influence on pork quality exists between breeds and within a breed. The variation is caused by a large set of genes and pork quality traits have a multi factorial background. Research into the genetics of meat quality found causative mutations associated with marked effects on pig meat value. The main objective of this study was to investigate the diversity of single nucleotide polymorphisms (SNPs) of meat quality-related genes in pigs from commercial and family farms in the North-West of Argentina. A screen for SNPs in RYR1, RN, CAST, and SOX6 candidate genes and the differentiation of their genotypes by PCR–RFLP was conducted. Results: All genes were characterized by a high level of polymorphism and heterozygosity. Additionally, both populations, commercial and Creole pigs, showed genetic closeness for the analyzed SNPs and a moderate selection for RYR1 and RN loci consistent with their allele´s adverse effects. Conclusions: The results obtained here highlighted the role of pig genotypes as a source of basic variability potentially affecting processed meat products as well as fresh meat.