Responses of drought tolerant lines (Mo’ko and Ollague) and drought susceptible lines (Ingapirca and Nariño) of Chenopodium quinoa (2n=4x=36) to water deficiency were assessed in two controlled drought stress experiments performed in the greenhouse: one being performed hydroponically using polyethylene glycol (PEG-8000) to impose drought and the other being performed in potting soil using a field capacity estimates to impose different amounts of drought. In the hydroponic experiment, all four cultivars were grown for 4-weeks when subjected to modified Hoagland solutions containing 0, 5, 10, 20, 30 or 40gL-1 PEG-8000 for a seven day period. Plants treated with more than 20gL-1 PEG-8000 were more damaged than those less than 20gL-1 PEG-8000. Drought tolerant lines were significantly shorter than the drought susceptible lines. In addition, Ollague showed a smaller stomatal conductance reading than both Ingapirca and Nariño cultivars. In the soil experiment, three cultivars (Ingapirca, Nariño and Ollague) were grown for 33-days when subjected to four different water treatments according to the calculated field capacity (FC): 100%, 50%, 30% and 10%FC for a 24-day period. Once again the drought tolerant cultivar (Ollague) was significantly shorter and had a smaller average leaf area than both Ingapirca and Nariño. Also, Ollague had a greater stem water potential. The lines however did not differ significantly in photosynthetic rate, stomatal conductance, transpiration rate or chlorophyll amount. We are using RNAseq to compare gene expression difference involved in the response to drought.