Development of local plant genetic resources grown in specific territories requires approaches that are able to discriminate between local and alien germplasm. In this work, three potato (Solanum tuberosum L.) local accessions grown in the area of Majella National Park (Abruzzo, Italy) and five commercial varieties cultivated in the same area were characterized using 22 morphological descriptors and microsatellite (SSR) DNA markers. Analysis of the DNA and of the plant, leaf, flower, and tuber morpho-agronomic traits allowed for a reliable discrimination of the local potato accessions, and provided a clear picture of their genetic relationships with the commercial varieties. Moreover, infrared spectroscopy was used to acquire a fingerprint of the tuber flesh composition. A total of 279 spectra, 70% of which were used in calibration and the remaining 30% for prediction, were processed using partial least squares discriminant analysis. About 97% of the calibration samples and 80% of the prediction samples were correctly classified according to the potato origin. In summary, the combination of the three approaches were useful in the characterization and valorization of local germplasm. In particular, the molecular markers suggest that the potato accession named Montenerodomo, cultivated in Majella National Park, can be considered a local variety and can be registered into the Regional Voluntary GR Register and entered into the foreseen protection scheme, as reported by the Italian regional laws.