Alexandrium minutum is a widely distributed HAB dinoflagellate that typically produces PSP neurotoxins (gonyautoxins 1,2,3,4), as well as poorly characterized allelochemicals. Within the EU-Project ESTTAL (Expressed Sequence Tags of Toxic Algae), we aim to identify candidate genes and processes putatively involved in toxicity and allelochemical interactions, and in growth regulation and stress responses. To obtain RNA samples linked with physiological status, batch cultures of A. minutum were grown under different environmental conditions, yielding differences in growth, PSP toxin production, and allelochemical potency. As a basis for gene expression analysis, we generated a normalized cDNA library, from which about 10,000 expressed sequence tags (ESTs) were generated. Annotation of these data yielded first insights into the genome of A. minutum. Based on the EST library, we designed an oligonucleotide microarray, which will be used to screen for differences in gene expression among the differently treated A. minutum cultures. Here we present the results of the EST library analysis, the design of the microarray, and physiological data of cultures grown for gene expression analysis.