Yacon (Smallanthus sonchifolius) is an asteraceous plant native to the Andes that in recent years has received special attention for its nutritional and pharmacological properties. Its roots store fructans of inulin type with low degree of polymerization, also called fructooligosaccharides (FOS). The loss of FOS in the yacon reserve structures and the consequent decrease of its functional properties are directly related to the hydrolytic activity of the enzyme fructanexohydrolase (FEH). Yacon plants were obtained from the "Baños del Inca" experimental station, belonging to the National Institute of Agrarian Innovation (INIA). By examining four methods of extracting total RNA from the storage roots, better performance and quality were obtained with the modified CTAB method the designed primer sets and the RT-PCR technique generated overlapping fragments of the feh gene, as well as the 3'-end of the mRNA. The assembly of the fragments allowed to determine about 80 percent of the gene sequence and a 3’untranslated region. Construction of the phylogenetic showed a high degree of identity of the sequence with the 1-FEHs of: C. intybus (88.5 %), H. tuberosus (88.2 %), V. herbacea 86.5 %) and A. lappa (85 %).