The Atlantic halibut (Hippoglossus hippoglossus) is a commercially important species, which due to historic overfishing and a high value is being developed as an aquaculture species. However there are currently issues in the efficient and successful supply of healthy juveniles for aquaculture production due to difficulties particularly in the first feeding stages and abnormal development during metamorphosis. Examples of such developmental problems include abnormal pigmentation (albinism, ambicoloration or mosaicism), failed migration of the left eye and skeletal deformities (reviewed in Power et al., 2008). Although the Atlantic halibut has been the subject of several traditional EST projects ( and ) and more recently Next Generation analyses into microRNAs ( and ), there is still a deficit with regard to the number of transcripts in the databases, which can be accessed and exploited for targeted candidate gene and pathway studies. In an effort to increase the genomic resources and underpin future molecular investigations into this species, we have generated a transcriptome drawing on RNA from the head, skin and gastrointestinal (GI-) tract using 454 pyrosequencing.