The dinoflagellate Alexandrium ostenfeldii is the only known producer of toxic spirolides. Spirolides are macrocyclic imines that are derived via polyketide biosynthetic pathways production is therefore almost certainly mediated by polyketide synthase (PKS) genes. At the genomic level, studies on the biosynthesis of protist-derived polyketides have been very sparsely reported. For dinoflagellates this is due in part to the pecularities of the dinoflagellate genome in both structural and regulatory respects. Our research focuses on the identification and characterization of genes involved in spirolide biosynthesis, specifically PKS genes. Genomic characterization of A. ostenfeldii was conducted by generating two Expressed Sequence Tag (EST) data banks, based on normalized cDNA libraries of two strains of A. ostenfeldii (AOSH1 and AOSH2) from Nova Scotia, Canada, which produce distinctive spirolide profiles. About 5.300 and 12.287 ESTs were sequenced which yielded in 2.634 and 9.833 unique sequences, respectively. The ESTs were annotated and compared between the two strains. Several genes putatively related to toxin synthesis were detected, including genes encoding PKS. A Fosmid library was also generated to detect and further analyse toxin-related genes. Significant insights into the general genomic organisation of A. ostenfeldii and the relationship with putative toxin-producing genes are expected. The identification of polyketide biosynthetic genes from dinoflagellates provide the first steps for further research on this pharmalogically interesting enzyme group.