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Citrus bacterial canker disease, caused by <i>Xanthomonas citri</i> subsp. <i>citri</i> (<i>Xcc</i>), poses a significant global threat to the citrus industry. <i>Lateral organ boundaries 1</i> (<i>Lob1</i>) is confirmed as a citrus susceptibility gene that induces pathogenesis by interaction with the PthA4 effector of <i>Xcc</i>. Citron C-05 (<i>Citrus medica</i>) is a <i>Citrus</i> genotype resistant to <i>Xcc</i>. However, there is little information available on the regulation of <i>Lob1</i> in resistant genotypes, which is important for the breeding of citrus cultivars resistant to canker disease. This study aimed to identify upstream regulatory factors of <i>Lob1</i> in Citron C-05 and to investigate its function in disease resistance. ‘Bingtang’ sweet orange (<i>C. sinensis</i>), a susceptible genotype, was utilized as the control. cDNA yeast libraries of <i>Xcc</i>-induced Citron C-05 and ‘Bingtang’ sweet orange were constructed. The capacities of ‘Bingtang’ and Citron C-05 were 1.896 × 10⁷ and 2.154 × 10⁷ CFU, respectively. The inserted fragments ranged from 500 to 2000 bp with a 100% recombination rate. The promoter of <i>Lob1</i> was segmented into two pieces and the P1 fragment from both genotypes was used to construct a bait yeast (PAbAi-<i>CsLob1</i>-P1; PAbAi-<i>CmLob1</i>-P1). Through library screening with the bait yeast, upstream regulators interacting with the <i>Lob1</i>-P1 promoter were identified and then validated using Y1H and dual-luciferase tests. The expression analysis of the three transcript factors indicated that RMA3 was upregulated by inoculation with <i>Xcc</i> in the resistant Citron C-05, but not in the susceptible sweet orange. The overexpression of <i>CsRMA3</i> in ‘Bingtang’ sweet orange led to reduced canker symptoms, with a significantly lower pathogen density in the leaves following <i>Xcc</i> inoculation. When <i>CmRMA3</i> was silenced by virus-induced gene silencing (VIGS) in Citron C-05, typical canker symptoms appeared on the <i>CmRMA3</i>-silenced leaves at 15 days post-inoculation with <i>Xcc</i>. Further expression analyses revealed that the CmRMA3 transcription factor suppressed the expression of <i>Lob1</i>. These results suggest that RMA3 participates in the resistant reaction of Citron C-05 to <i>Xcc</i> infection, and such a response might be in relation to its suppression of the expression of the pathogenic gene <i>Lob1</i>.