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The tangerine pathotype of <i>Alternaria alternata</i> produces the <i>Alternaria citri</i> toxin (ACT), which elicits a host immune response characterized by the increase in harmful reactive oxygen species (ROS) production. ROS detoxification in <i>A. alternata</i> relies on the degradation of peroxisomes through autophagy and iron acquisition using siderophores. In this study, we investigated the role of autophagy in regulating siderophore and iron homeostasis in <i>A. alternata</i>. Our results showed that autophagy positively influences siderophore production and iron uptake. The <i>A. alternata</i> strains deficient in autophagy-related genes 1 and 8 (ΔAa<i>atg1</i> and ΔAa<i>atg8</i>) could not thrive without iron, and their adaptability to high-iron environments was also reduced. Furthermore, the ability of autophagy-deficient strains to withstand ROS was compromised. Notably, autophagy deficiency significantly reduced the production of dimerumic acid (DMA), a siderophore in <i>A. alternata</i>, which may contribute to ROS detoxification. Compared to the wild-type strain, ΔAa<i>atg8</i> was defective in cellular iron balances. We also observed iron-induced autophagy and lipid peroxidation in <i>A. alternata</i>. To summarize, our study indicates that autophagy and maintaining iron homeostasis are interconnected and contribute to the stress resistance and the virulence of <i>A. alternata</i>. These results provide new insights into the complex interplay connecting autophagy, iron metabolism, and fungal pathogenesis in <i>A. alternata</i>.