ISJ 8: 179-189, 2011 ISSN 1824-307XREVIEWGene expression studies largely support the understanding of gene-environment interactions in humans and other living organisms but the lack of genomic and genetic information often complicates the analysis of functional responses in non-traditional model species. Nevertheless, the fast advancement of DNA microarray and sequencing technologies now makes global gene expression analysis possible in virtually any species of interest. As regards the Mytilus genus, tens of thousands Expressed Sequence Tags (ESTs) are currently available for M. californianus and M. galloprovincialis, and DNA microarrays have been developed. Among them, Immunochip 1.0 specifically includes 1,820 probes of genes centrally involved or modulated in the innate immune responses of the Mediterranean mussel. This review recalls peculiarities and applications of the existing mussel DNA microarrays and finally summarizes facts concerning a variety of transcript sequences likely involved in the mussel immunity. Beside DNA microarrays, Next Generation Sequencing (NGS) technologies now offer new and broader research perspectives, from the whole transcriptome coverage to the Mytilus genome sequencing.