A wave of public information has enabled the report of innumerable examples where transposable elements (TEs) fragments are incorporated as exons into mRNAs, however, the proposition that such exonized TEs encode functional proteins is controversial. In order to characterize the gene expression pattern of TE-derived coding sequences identified in the Coffea arabica genome, we analyzed the macroarray profiling and digital northern of transcripts with distinct molecular functions of sequences containing TE-cassettes or not. The evolutionary changes of the gene expression pattern mediated by exonized TE sequences using probes of tissues and stress conditions derived from C. arabica and C. canephora are presented and discussed.