Coffee is one important agricultural product to several developing countries. It is mainly produced by the allotetraploid Coffea arabica and the diploid C. canephora. Meanwhile, Coffea eugenioides is considered the ancestor of allopolyploid Coffea arabica, together with C. canephora, but there are few molecular studies in this specie. In this work, we present a large scale gene identification of C. eugenioides from RNA-Seq. A de novo assembled with all sequences was performed by Trinity and it generated 36,935 contigs which were successfully annotated against non-redundant (NCBI-nr) p rotein database, GO, Swiss-Prot, InterproScan, PlantCyc and KEGG. In addition, we examined genes differentially expressed in leaves and fruits of C. eugenioides using DESeq. A set of genes related to sugar metabolism and fruit ripening were identified in b oth organs. Finally, 10 highly expressed genes were selected to confirm their expression pattern by qPCR. Our study provides novel information to C. eugenioides and it is a valuable source for molecular and genetics studies for Coffea and can increase our knowledge about the mechanisms involved in the C. arabica homeologs expression. This general repertoire of C. eugenioides genes could open new perspectives to develop studies in this specie as well as the genetic improvement of commercial coffee.