The Andean farmer conserves and maintains the existing genetic diversity of potato cultivars by means of clonal propagation of tubers. However, surveys of traditional farms showed that botanical seed propagation was used for disease elimination, stock rejuvenation and the creation of new cultivars. Electrophoretic surveys based on 542 tubers collected from 18 markets sampled in the Cusco area disclosed a total of 229 different cultivars from diploid, triploid and tetraploid forms of Solanum tuberosum L. These could be classified by isozyme cluster analysis into four major groups and six minor groups. However, they did not agree with groups based on flesh or skin color. It is therefore concluded that all genotypes belong to a single, large gene pool with considerable gene flow between cultivars of different groups. When the samples were grouped by the three most common tuber skin colors, namely red/pink ('Q'ompis type'), purple ('Yana Imilla' type), and yellowish/brown ('Yuraq Kusi' type), similar allozymes were observed in all three classes. The structure of the isozymic phenotypes within each group indicate that they may have been derived as segregants after outcrossing of diverse parental types. In order to provide further evidence for the origin of new types by hybridization, two segregating diploid progenies were generated by crossing purple by yellow skin types. In the resulting F1, most of the tuber phenotypes observed in the Andean varieties were reproduced in these crosses. It can be concluded that the Andean potatoes form a large and plastic gene pool amplified and renovated by outcrossing followed in some cases by human selection of desirable phenotypes. © 1992 Kluwer Academic Publishers.