Isopods of the genus Idotea have an unusual ability to feed on algae containing high amounts of chemical defense molecules, such as Fucus and Ulva. In this study, we compare gene expression patterns of Idotea balthica individuals fed with F. vesiculosus to individuals fed with U. lactuca. We generate the first-ever transcriptome assembly for this species, and find 3,233 differentially expressed genes across feeding regimes. However, only a handful of biological functions are enriched with regards to differentially expressed genes, the most notable being “alkaloid metabolic process”. Within this category, we find eight differentially expressed cytochrome P450 (CYP) unigenes, all of which have a higher expression in the U. lactuca diet treatment. A phylogenetic analysis shows that the differentially expressed CYP genes are closely related to a CYP gene described from the hepatopancreas of the spiny lobster Panulirus argus, and we hypothesize that these transcripts are involved in metabolite detoxification. This is a first step in the understanding of this algae-grazer interaction, and will form a basis for future work to characterize cytochrome P450 functioning in marine crustaceans.