The technologies used for transcriptome studies have rapidly evolved during the last two decades, becoming more powerful and less expensive. In this post-genomic era, deep understanding of gene expression, regulation and co-expression in tissues during developmental processes or in response to biotic and/or abiotic constraints as related to changing environmental conditions is crucial. Moreover, transcriptomics represents also a yet-underexplored source of molecular information for developing molecular markers, particularly useful in species with large genomes rich in repetitive sequences. In this chapter we briefly review the history and state of transcriptomic technologies and data analysis tools, with particular emphasis on the challenges posed by the tetraploid durum wheat, and we review some original publications that used transcriptomic analysis for deciphering gene expression during seed development, stress response or for the identification of varietal-specific SNPs.