The marine dinoflagellate Alexandrium ostenfeldii is a harmful algae with global distribution and is the causative producer of spirolides, a potent neurotoxin in rodents. Spirolides are thought to be produced by polyketide synthases (PKS) based on their chemical structure which is further confirmed by the presence of PKS candidates in an A. ostenfeldii expressed sequence library. Here, five PKS full lengths mRNA transcripts were obtained in A. ostenfeldii by rapid amplification of cDNA ends with polymerase chain reaction. The transcripts are characterized by the presence of polyadenylation, 3’ untranslated regions and the dinoflagellate-specific spliced leader sequence at the 5’end of PKS transcripts. One transcript encoded for an acyl carrier protein adjacent to a protein-protein binding domain, two ketoreductases and two transcripts encoded for ketoacyl synthases (KS). The two KS contain long N- and C-terminal regions unique to dinoflagellates which are flanking the central ketoacyl synthase domain. Four conserved sites could be identified in the N-terminal region but the function could not be predicted. A Maximum Likelihood phylogenetic analysis of A. ostenfeldii KS domains placed them well within the protist Type I PKS clade between apicomplexa, haptophytes and chlorophytes and formed a clade with the dinoflagellate Karenia brevis KS. Recent findings for K. brevis KS suggest a novel monofunctional organization like in Type II PKS, despite their evolution being derived from Type I PKS for dinoflagellate PKS. The results obtained here support this idea and the monofunctional organization of A. ostenfeldii was further confirmed by a preliminary Western Blot. The conserved sites N-terminal identified here could be applied to mine for new dinoflagellate KS gene candidates in metagenome data. Concerning the spirolide biosynthesis, an iterative use of PKS proteins is conceivable in dinoflagellates despite of their modular origin.