Indigenous biosystematics consists of subsystems of folk taxonomy, descriptor use and nomenclature. Folk taxonomy of Andean potatoes recognizes at least five ranks. The folk generic rank is composed of three taxa: Araq Papa (semi-wild/consumed), Papa Tarpuy (cultivated/consumed) and Atoq Papa (wild/not consumed). Folk specific taxa (= cultivar groups) and varietal taxa (= landraces) are abundant within the generic taxon of Papa Tarpuy. Use categories and agroecological criteria do not constitute main differentiating factors. Folk varietal taxa cluster well when using formal morphological descriptors; folk specific taxa less so. A moderate correlation, albeit with considerable exceptions, exists between folk specific or varietal taxa and their genetic make-up as characterized with molecular markers (18 SSR microsatellites). The coherence of clustering in a dissimilarity tree (dendrogram) varies for each folk specific (nine) or varietal taxon (two) considered. Farmers use a repertoire of 22 plant and 15 tuber descriptors, each with specific character states in the Quechua language. Farmers are well able to recognize specific landraces based on aboveground plant parts only (without exposing tubers). Nomenclature is regionally consistent for common landraces, while inconsistent for scarce landraces. Primary landrace names (nouns) generally refer to a folk specific taxon through predominant metaphorical reference to tuber shape. Secondary landrace names (adjectives) predominantly provide direct reference to tuber color.