Marine dinoflagellates of the genus Alexandrium are well known for their ability to produce the potent neurotoxin saxitoxin and other analogues responsible for paralytic shellfish poisoning (PSP). Dinoflagellates are the only known eukaryotes confirmed to produce these neurotoxins, but they are also synthesized by certain brackish and freshwater cyanobacteria giving rise to speculations about their prokaryotic origin. Thus far, no distinct enzymes or genes involved in the actual synthesis of the toxins have been unequivocally identified in either dinoflagellates or cyanobacteria. However, detailed proposals for such a pathway exist, and the requirements for biosynthesis have been examined in vitro. In order to contribute to the search for genes involved in PSP toxin production, we developed a DNA microarray based upon an expressed sequence tag (EST) library from A. minutum. This species tends to produce a limited sub-set of PSP toxins, typically dominated by the sulfated carbamate derivatives known as gonyautoxins. The array was used in gene expression studies involving both toxic and non-toxic A. minutum strains, as well as different physiological conditions within one strain. We identified genes associated with the ability to produce PSP toxins in an inter-strain comparison. Here we compare these data to gene expression correlated with differences in toxicity under different physiological conditions.