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Coffee, a widely consumed important agricultural product, is mainly produced from two species, <i>Coffea arabica</i> (Arabica coffee) and <i>C. canephora</i> (Robusta coffee). Timor Hybrid (HDT) is a population resulting from a natural cross between <i>C. arabica</i> and <i>C. canephora</i>. HDT derivatives have a high spectrum of resistance to different races of <i>Hemileia vastatrix</i> (Hv), the causal agent of coffee leaf rust. A RNAseq database, obtained from HDT832/2 leaves inoculated with Hv (Host Resistance) and <i>Uromyces vignae</i> (Uv, Nonhost Resistance), showed the presence of genes implicated in the hypersensitive response and salicylic acid pathway. Hypersensitive Induced Reaction (HIR) gene family, Enhanced Disease Susceptibility1 gene (EDS1), and Phytoalexin Deficient 4 (PAD4) gene are involved in host and nonhost resistance. Relative expression calculated by RT-qPCR was used to confirm and expand the transcriptome analysis. <i>HDTHIR4</i>, <i>HDTEDS1</i>, and <i>HDTPAD4</i> showed the highest upregulation in response to Hv and Uv inoculation, confirming a similar trend in host and nonhost resistance in HDT. HIR and EDS1/PAD4 gene families were characterized for the first time in the three available <i>Coffea</i> genomes. HIR genes were quite conserved between <i>Coffea</i> species. Surprisingly, EDS1 and PAD4 genes revealed major differences in gene structure. The PAD4 predicted protein from <i>C. arabica</i> does not include both conserved domains of the EDS1/PAD4 family, and the EDS1 putative protein from <i>C. canephora</i> includes a formin domain unusual in the same protein family. The variability shown by EDS1/PAD4 gene family may impact the disease resistance response of <i>Coffea</i> species, which can be surveyed for the gene sequences that will produce a more resistant phenotype.