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Water shortage is a critical problem touching plant growth and yield in semi-arid areas, for instance the Mediterranean region. For this reason was studied the physiological basis of drought tolerance of a new, drought tolerant crop quinoa (Chenopodium quinoa Willd.) tested in Morocco in two successive seasons, subject to four irrigation treatments (100, 50, and 33% ETc, and rainfed). The chlorophyll a fluorescence transients were analyzed by the JIP-test to translate stress-induced damage in these transients to changes in biophysical parameter’s allowing quantification of the energy flow through the photosynthetic apparatus. Drought stress induced a significant decrease in the maximum quantum yield of primary photochemistry (phi(P0) = F-v/F-m), and the quantum yield of electron transport (phi(E0)). The amount of active Photosystem II (PSII) reaction centers (RC) per excited cross section (RC/CS) also decreased when exposed to the highest drought stress. The effective antenna size of active RCs (ABS/RC) increased and the effective dissipation per active reaction centers (DIo/RC) increased by increasing drought stress during the growth season in comparison to the control. However the performance index (PI), was a very sensitive indicator of the physiological status of plants. Leaf area index, leaf water potential and stomatal conductance decreased as the drought increased. These results indicate that, in quinoa leaf, JIP-test can be used as a sensitive method for measuring drought stress effects.