Purple- and red-fleshed potato cultivars constitute a great source of phenolic compounds, which may promote human health. Since the characterization of potato germplasm is a key step during the breeding process, the classification of high anthocyanin-producing tetraploid genotypes may facilitate the incorporation of phenolic-related traits in a potato breeding programme. A set of 18 high anthocyanin-producing underutilized tetraploid cultivars, which have been previously classified in terms of phytochemical content, have been characterized by both microsatellite markers (simple sequence repeat, SSR) and morphological descriptors. A wide genetic variability was found using 11 highly discriminatory SSR markers. The collection also displayed a large amount of variation for most morphological traits. The neighbour-joining trees defined by SSR markers and morphological descriptors revealed genetic and phenotypic relatedness of the potato genotypes. Despite the complexity of tetrasomic inheritance, high anthocyanin-producing tetraploid cultivars should be considered for potato breeding since they are adapted to long-day conditions and do not present undesirable characteristics that are found in native accessions or landraces.