The use of analytical methodologies based on DNA (e.g. PCR-RFLP) to determine the authenticity of different types of meat products after the initial labeling is pivotal to avoid fraudulent practices due to the increased rates of meat consumption. Our PCR-RFLP of mitochondrial 12S rRNA gene using restriction enzymes (AluI and ApoI) aimed to confirm the accuracy of the meat species labeling, based on fresh and processed meat collected in central markets along the main cities in the Amazonas Region (Bagua, Bagua Grande, Chachapoyas, Luya, Pedro Ruiz, Rodriguez de Mendoza). Our analyses qualitatively identified and differentiated three commercial species of fresh meat (bovine, porcine, ovine) and also found the substitution of goat by sheep meat. Regarding processed meat, its composition was uncertain and further analyses should be addressed to determine the meat origin. Monitoring using DNA-based analytical methods of meat trade is suggested to determine fraudulent practices, such as species substitution in markets along regions of Peru.