Chemical ecology in marine systems is less understood than in terrestrial systems. Nevertheless, even such simple organisms as unicellular marine microalgae use secondary metabolites for defense, prey acquisition, induction of sexuality or life cycle transitions. With the example of the toxic species Alexandrium ostenfeldii we apply an interdisciplinary approach using molecular, biological, toxicological and analytical tools towards the functional understanding of secondary metabolites of A. ostenfeldii as well as its ecological effects. Information on the expressed genome has been gathered by creating expressed sequence tag (EST) libraries and comparing the sequence data with known sequences from gene bank. Polyketide synthase (PKS) genes have been identified, which are responsible for the biosynthesis of spirolides, a class of macrocyclic imine neurotoxins synthesized by A. ostenfeldii. This group of toxins, including new analogues has been detected by liquid chromatography-tandem mass spectrometry coupling (LC-MS/MS). Spirolide cytotoxicity has been examined with mouse neuroblastoma cell cultures and assays on alleochemical effects of extracellular metabolites of A. ostenfeldii on other marine protists have been performed. This interdisciplinary research has contributed substantially to understanding the relationship between genetic expression of macrocyclic imine toxins and their toxicological mode of action.