Botanical species and morphological and genetic diversity represent different yet linked units of conservation. These features, and their spatial distribution in the central Peruvian Andean highlands of Huancavelica, were used as a basis for characterizing and quantifying potato agrobiodiversity at different scales. Results show that individual farm households maintain high levels of cultivar, morphological, and genetic diversity. At the regional level, all cultivated species, with the exception of Solanum ajanhuiri, were found to be present. Tetraploid native potatoes were most abundant, followed by diploids, triploids, and pentaploids. Morphological characterization of 2481 samples belonging to 38 in situ collections resulted in the identification of 557 unique cultivars. Genetic fingerprinting of 989 samples belonging to 8 in situ collections resulted in the identification of 406 unique cultivars. The principal source of genetic variation is found within rather than between geographically distanced subpopulations. High levels of cultivar diversity are found, particularly at elevations between 3850 and 4150 m.