A set of 15 maca and 25 yacon genotypes cultivated under field conditions were assessed as to relationships between morphotypes of underground organs, yield parameters, and polymorphism of isozymes. In vitro cultivation and the content of some chemical compounds were also studied. Underground organs of both crops showed a wide variety strongly dependent on environmental factors. The results showed that maca forms small-weight hypocotyls. Differences in chemical composition compared with a commercial source were observed. The highest production (3.8 kg/plant) of yacon tubers was observed in four genotypes. Drying of yacon chips was found to be a good method of preservation. Of 17 analysed enzymatic systems, only esterases showed some degree of polymorphism in both crops, dividing genotypes of maca into two and yacon into six groups. Polymorphism of esterases does not correspond with morphological characters of underground organs of both crops or with total phenolic contents in different genotypes of yacon leaves. Screening of cultivation media demonstrated that concentration of regulators must be optimised to be suitable for in vitro cultivation of maca. The results showed that yacon can be successfully cultivated in Europe in contrast to maca.