The cosmopolitan marine dinoflagellate Alexandrium minutum is known to produce toxins causing paralytic shellfish poisoning (PSP). As has recently been shown, this toxicity can be enhanced by the presence of certain copepod species. Inducible defences are known from a variety of marine organisms, but the associated transcriptomic changes have only been investigated in model angiosperms. Here, we use a microarray approach to investigate the changes in gene expression during the copepod-provoked induction of higher toxicity in A. minutum. We found a limited set of 14 genes (0.35% of the tested sequences) to be affected by copepod presence; gene expression changed by a factor of 1.9 to 11.4 when compared with control samples. We compared the differentially expressed genes after one day–before the onset of augmented toxicity–and after 3 days, when cellular toxin content in the induced samples was five times higher than in control cultures. Comparison with differences previously found between toxic and non-toxic strains revealed two sequences apparently associated with PSP toxin content. Our study is the first investigation of transcriptomic effects associated with grazer-induced induction of elevated toxicity in a protist. This provides a novel approach to the ecology of predator–prey interactions, as well as a highly targeted method for investigating the genes associated with toxin production and regulation in toxic dinoflagellates. © 2011 Taylor & Francis Group, LLC.