Paralytic shellfish poisoning (PSP) toxins are among the most potent and pervasive biotoxins for humans, animals and aquatic ecosystems worldwide. The neurotoxic alkaloids are produced by both cyanobacteria (prokaryotes) and marine dinoflagellates (eukaryotes). This review focuses on the biosynthetic pathway of PSP toxins and its evolutionary history. The identities of the biosynthetic genes have been recently studied in several cyanobacteria that are capable to produce PSP toxins. However, less is known about the evolution of the biosynthetic pathway in dinoflagellates. It remains to be elucidated whether the pathway arose independently or whether the eukaryotic genes originate from a prokaryotic ancestor by horizontal gene transfer. This review provides an overview about recent scientific findings concerning the ecophysiological impact of PSP toxin biosynthesis for the producing organisms. Furthermore, the phylogentic relation of this unique and complex biosynthetic pathway is discussed for both lineages. This includes the occurrence of toxic and non-toxic strains within one species of cyanobacteria and dinoflagellates. Finally, the discussion of future prospects provides an outline about open questions that remains to be investigated.