Citrus canker (Xanthomonas axonopodis pv. citri) has brought great damage to citrus industry worldwide. To control the disease, it seems the use of resistant genotypes is the only choice. A total of 14 accessions from three species were investigated by artificial inoculation of leaves with the pathogen, and it was found that only chinese citron (C. medica) showed complete and active resistance to canker disease.To elucidate the functional complexity of its transcriptome , Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of chinese citron. With the high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight into its transcriptome. We were also able to assess the alternative mRNA isoforms in chinese citron and found a large number of genes undergoing alternative splicing. Many genes and pathways that might be involved in higher levels of protein production in artificial inoculation than in control were identified by comparing gene expression levels. Our analysis indicated that the transcriptome of chinese citron is much more complex than previously anticipated, and these results may provide a blueprint for further study of the citrus transcriptome.