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A set of 15 accessions of maca, Lepidium meyenii Walp., and 25 accessions of yacon, Smallanthus sonchifolius (Poepp. & Endl.) H. Robins., cultivated under Czech field conditions was studied to determine relationships between morphological variability and isozyme polymorphisms. Morphological characterisation of maca included evaluation of length, weight, shape, skin and flesh colour of hypocotyls. In yacon, we evaluated shape, colour, skin texture and flesh colour of tubers, as well as the number of roots. Preliminary results showed that maca forms low-weight hypocotyls (up to only 17.4 g) under Czech field conditions. For yacon, tuber production ranged between 1.4 kg and 3.8 kg. Of the 17 analysed enzymatic systems, only esterase (EST) showed some degree of polymorphism in both crops. It was possible to divide accessions of L. meyenii into two groups and S. sonchifolius into six groups on the basis of isozyme polymorphisms. However, EST polymorphisms do not correspond very well to the morphological characteristics of the underground organs of the crops studied.