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Plants have developed mechanisms to protect themselves against both biotic and abiotic environmental stress. Specialized/secondary metabolism is one of the stress response mechanisms. Recently, we reported that flavonoids, a class of specialized metabolites, including flavonols and anthocyanins with strong radical scavenging activity contributed to the mitigation of oxidative and drought stress in Arabidopsis thaliana (Arabidopsis). However, the behavior of flavonoids during drought stress is still not well-documented. Herein we investigated the time-series alternation of flavonoids in the aerial part of Arabidopsis (wild type, Col-0) during drought stress by LC-QTOF-MS. The drastic alternation of 5 flavonols and 5 anthocyanins was revealed together with changes in marker metabolites of drought stress, e.g., proline, raffinose, and galactinol. These findings indicate that flavonols and anthocyanins can mitigate …