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Although crosstalk between cytosolic and plastidic terpenoid pathways has been validated in many plant species, we report here for the first time a striking elevation of the nucleus-encoded artemisinin biosynthesis relevant DBR2 mRNA following the incubation of plants with fosmidomycin (FM). FM decreased singlet oxygen (1O2) scavengers such as β-carotene and α-tocopherol and subsequently invoked 1O2 burst. The treatment of plants with fluridone (FD) neither decreased α-tocopherol content nor triggered 1O2 emission. In conclusion, FM can up-regulate 1O2-sensitive nuclear genes responsible for artemisinin biogenesis by mitigating the accumulation of plastidic scavenging terpenoids, thereby eliciting 1O2 generation and initiating 1O2 retrograde signaling.