Quinoa (ChenopodiumquinoaWilld.) is a highly nutritious Andean seed crop which shows great potential to grow under a range of hostile environments. The objective of this study was to investigate the differences of drought tolerance of a Bolivian (Achachino) and a Danish (Titicaca) variety, and especially drought-related adaption strategies. Soil water status was expressed as the fraction of transpirable soil water (FTSW). Relative stomatal conductance (RSC), relative transpiration (RT) and relative leaf water potential (RLW) were calculated by determining stomatal conductance, transpiration rate and leaf water potential of the drought-treated plants relative to those of fully irrigated plants. The responses of RSC, RT and RLW to decreasing FTSW were described by a linear-plateau model. The critical value of FTSW was the threshold of FTSW where the parameters studied decreased. The thresholds increased CS for stomatal conductance, CT for transpiration and CLfor leaf water potential. Achachino showed significantly lower CT and CL when compared with Titicaca, implying that transpiration and leaf water potential were less affected under mild drought conditions in the Bolivian variety. CS in Achachino was significantly higher than CL and CT, which indicated that stomatal conductance declined before transpiration and leaf water potential were reduced. Such difference was found in Titicaca where reduction of leaf area had more effect on transpiration than stomatal closure. Slower growth rate and smaller leaf area in combination with a lower stomatal conductance was found to contribute to drought resistance in Achachino. ABA concentration in the xylem sap tended to increase in both varieties after 2 days onset of drought, prior to decline in leaf water potential. Titicaca showed significantly (P < 0.05) higher ABA concentration when compared with Achachino under both fully irrigated and drought conditions. Titicaca had higher xylem nutrient concentration in comparison with Achachino in both fully-watered and drought plants at day 2 after onset of soil drying. It was concluded that Titicaca was more sensitive to progressive drought than Achachino which avoided water loss by means of lower growth rate and smaller leaf area.