The coffee berry borer (CBB) is the most prevalent pest of coffee plantations. Within the Coffea genus, C. arabica is susceptible to CBB and C. liberica shows a lower susceptibility. Two EST libraries were constructed from the total RNA of C. arabica and C. liberica fruits artificially infested with CBBs for 24 h. Using 6000 clones sequenced per library, a unigene database was generated, obtaining 3634 singletons and 1454 contigs. For each contig, the proportion of sequences present in both species was determined and a differential gene expression between the species was detected. C. arabica displayed a higher relative expression of proteins involved in general stress responses, whereas C. liberica showed the induction of a higher number of insect defense proteins. In order to validate the results, quantifications through real-time PCR were done. A hevein-like protein, an isoprene synthase, a salicylic acid carboxyl methyltransferase and a patatin-like protein gene were highly upregulated in C. liberica at 24 and/or 48 h after insect infestation compared to C. arabica. The identification of metabolic pathways induced by this pest insect provides tools to take advantage of the genetic resources available for the control of CBB.