Alexandrium tamarense forms harmful algae blooms associated with a phenomenon called Paralytic Shellfish Poisoning in costal, temperate waters („Red Tides“). Reducing mortality caused by grazing to a minimum through active deterrence/defence against the predator increases the possibility of achiving positive growth rates for bloom development. Copepods are one of the major grazers in costal systems and Alexandrium cells showed a significant higher PSP-toxin content when exposed to different copepods, or their waterborne cues. The effect from grazers and/or their cues on Alexandrium cells using a microarray platform designed from several Alexandrium species EST databanks was further analyzed on a transcriptomic level. On this basis it was possible to identify a common set of genes showing regulation even in cases where no higher PSP-toxin content was measureable. These results indicate that a perception of waterborne cues from different copepods exists, and that it is measureable through global gene expression patterns. Given these facts, a subtracted cDNA-library from diverse induction experiments with different species interacting with Alexandrium was constructed. This is a promising approach to further analyze the genomic cascade behind induced defence and species interaction through waterborne cues in phytoplankton.