Cyanobacteria enter into various symbiotic interaction with a wide spectrum of organisms distantly related to the tree of life. The level of proximity varies immensely in these interactions. As many other prokaryotes, the majority of cyanobacterial strains possess synthetic machineries of employing non-ribozomal peptide synthetases, and polyketide synthetases, which can be combined to produce a large diversity of chemical structures from low-molecular alkaloids up to large peptides. Some of the resulting compounds, as for example, well known heptatotoxic peptides microcystins, were intensively studied in the past decades for their adverse effect on many organisms, including human. Recent studies show that despite their adverse effect on many organisms, some secondary metabolites are produced frequently by cyanobacteria in symbiotic interactions. This fact is raising important questions concerning the possible role of cyanobacterial metabolites in symbioses. Moreover, as the link between production of neurotoxic β-methylamino-L-alanine (BMAA) by symbiotic cyanobacteria and human neurodegenerative diseases has been proposed in the case Guam population in Micronesia, symbiotic cyanobacteria seems to be important also from a toxicological point of view. This chapter is reviewing some currently known cases of symbiotic interaction where cyanobacterial secondary metabolites are produced within the association – microcystin and nodularin production in lichen and higher plants, production of various peptides in marine sponges, and production of neurotoxic BMAA by symbionts of Cycas and other higher plants.