Quinoa is a traditional Andean seed crop highly tolerant to abiotic stresses. Since most seed crops cultivars are sensitive to drought stress, quinoa is considered as a valuable candidate for severe environmental conditions to which the plant is exposed. In this study we focused on the impact of hydropriming on drought tolerance in three quinoa cultivars (Q26, Q29 and Titicaca) in two arid regions of Iran. We observed that, under field conditions, quinoa responded to drought stress with a significant decrease in growth, yield component, seed yield and biochemical traits including photosynthetic pigments and relative water contents. In contrast, malondialdehyde, electrolyte leakage and proline concentration in all quinoa cultivars in both regions increased. However, seed priming significantly improved growth and seed yield. The results of the correlation analysis revealed that seed yield was highly positively related to pigments and proline concentration. Therefore, it could be suggested that these traits are efficient and reliable indicators for indirect selection of tolerant quinoa cultivars under drought stress conditions. In general, Q26 and Q29 were considered as superior cultivars for well-watered conditions and Titicaca cultivar was found relatively more drought tolerant than other cultivars. This study may contribute to the understanding of seed priming could be applied as an efficient approach to ameliorate the adverse effects of drought stress in quinoa cultivars.