The mussel Mytilus galloprovincialis is an important aquaculture resource. Bivalve molluscs are filter feeding species that can accumulate biotoxins in their body tissues during harmful algal blooms. Amnesic Shellfish Poisoning (ASP) is caused by species of the diatom genus Pseudo-nitzchia, which produces the toxin domoic acid. We assembled de novo the transcriptome of Mytilus galloprovincialis digestive gland and we investigated the genes differentially expressed after exposure to domoic acid-producing Pseudo-nitzschia australis, in order to examine the genes altered by the action of domoic acid, and to identify genes that could participate in the detoxification process.