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Plant defense and development are intricately interconnected. The putative RNA binding protein FLOWERING LOCUS K HOMOLOGY DOMAIN (FLK) was previously shown to play a critical role in regulating pathogen defense and flowering time in Arabidopsis. However, the molecular basis underlying the multifunctionality of FLK remains to be determined. Here we provide data to support a role of FLK in regulating reactive oxygen species (ROS) homeostasis, which is dependent on the primary catalase gene CAT2. The flk mutations confer reduced ROS burst upon elicitation and higher resistance to ROS-inducing stress conditions, including treatments with the herbicide paraquat, UV, and salinity. CAT2 is required for flk-conferred abiotic stress response and pathogen defense. We further demonstrate a negative regulation of the catalase enzyme activity by FLK. In addition, our data show that the ROS-regulatory role of FLK is independent of its function in flowering time control. Together our data illustrate a mechanism underlying FLK’s defense role and decouple the multifunctionality of FLK in defense and development in Arabidopsis.