European sardine is a planktonik small pelagic of great economical and nutritional importance. However, low catches and recruitment failures of the fisheries of this species have been recently reported. However, due to the scarcity of genomic resources available for this species, it is not possible to detect if such population decrease has leaded to an ecological risk from the conservation genetics perspective. To address this problem, we describe for the first-time this species’ transcriptome, by sequencing ten different tissues.