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Citrus canker is a quarantined disease caused by the bacterial plant pathogen <i>Xanthomonas citri</i> subsp. <i>citri</i> (<i>Xcc</i>), which causes persistent surface damage, leaf and fruit drop, and tree decline in citrus plants. The citrus cultivar Citron C-05 (<i>Citrus medica</i> L.) is a disease-resistant genotype identified after years of screening at the National Center for Citrus Improvement (Changsha), which displays allergic, necrotic, and disease-resistant responses to <i>Xcc</i>. In this study, the <i>BAK1</i> gene was identified in this cultivar to be a disease resistance gene involved in plant-microbe interaction between citrus and <i>Xcc</i>. Functional investigations of this gene revealed that both <i>CsBAK1</i> <i>(C. sinensis</i> <i>BAK1</i>) or <i>CmBAK1(C. medica</i> <i>BAK1</i>) could inhibit the growth of <i>Xcc</i> to some extent when transiently expressed in the susceptible ‘Bingtang’ genotype of sweet orange. Critical regions of the <i>CmBAK1</i> promoter sequence were identified by creating downstream deletions and exposing mutants to <i>Xcc</i> to determine effects on the resistance phenotype; a 426 bp region (−2000~–1574) was identified as a key functional region responsible for eliciting the hypersensitive response in plants. Through screening arrayed Citron C-05 cDNA libraries by yeast one-hybrid assays, a basic APETALA2/ETHYLENE RESPONSE FACTOR (AP2/ERF) transcription factor of <i>CmRAP2-13</i> that binds directly to the 426 bp key sequence and activates expression of <i>CmBAK1</i> was identified. Moreover, transcriptional analysis revealed an obvious increase in transcript levels of <i>CsRAP2-13</i> in Citron C-05, American citron, and Finger citron. In this study, we present the identification of transcriptional activators that are found to interact with BAK1 proteins in response to <i>Xcc</i>. These results reveal a coordinated regulatory mechanism of RAP2-13, which may be involved in defence responses through the regulation of BAK1.