Toxic marine algae increasingly cause problems worldwide by forming so called harmful algal blooms (HABs). Although growth, taxonomic composition and diversity, ecophysiology and biomass transfer are well understood, few is known about the chemical interactions on species level, which are responsible for the regulation of growth, competitive factors and species succession. The ecological chemistry group at the AWI starts an interdisciplinary approach towards the understanding of these interactions of single protist species. The interdisciplinary approach consists of competition and survival experiments for the detection and investigation of allelochemical interactions among protist species, genetic and molecular biological methods for the analysis of gene expression and function of involved genes, and finally analytical chemical methods for the detection and quantitation of secondary metabolites that mediate these effects. A short overview over some currently ongoing projects will be given.