One of the largest and most diverse clonally propagated potato collections of cultivated potato species is maintained at the International Potato Center (CIP). Almost 75% of this collection is S. tuberosum subsp. andigena (hereafter andigena) cultivars. The first step to select a core collection of this subspecies was to identify duplicate accessions of the same cultivar using comparisons of morphological characters and electrophoretic banding patterns of total proteins and esterases. This reduced the number of accessions in the collection from 10,722 to 2,379. The number of accessions of the same cultivar in the original collection ranged from 1 to 276. This is a report on the selection of a core from the 2,379 morphologically different cultivars using morphological, geographical, and evaluation data. A total of 25 morphological descriptors were scored from all 2,379 andigena cultivars. A phenogram was constructed from these data using a simple matching coefficient and the unweighted pair group method using arithmetic averages. We decided to include in the core a proportional sample consisting of approximately the square root of the number of accessions from each first geographical division (state, department, or province) of countries where andigena was collected. Accessions were chosen first to represent the widest morphological diversify and to maximize geographical representation of the clusters distributed on the main branches of the morphological phenogram. Second, the representative accession of each cluster was also chosen considering data on resistance to diseases and pests, dry matter content, and number of duplicate accessions identified in the original collection. The resulting core has 306 accessions (12.86%) from eight countries from Mexico to Argentina. The full breeding potential of Andean farmer-selected potato cultivars that have been maintained for centuries in their center of diversify remains unknown. A thorough evaluation of their reaction to diseases and pests and other desirable traits is now feasible because the selected andigena core set covers the broadest genetic base that is available in ex situ conservation.