This chapter deals with the main cyanobacterial toxins that affect the marine environment, including brackish waters in estuaries or the Baltic Sea. In the marine environment, cyanobacterial toxins have been associated with human and animal intoxications more seldom, except with the cases of Moorea producens associated toxins that may cause the "swimmer's itch". The chapter reviews the main cyanobacterial toxins with importance in the marine environment with special emphasis on the main sources, chemistry, toxicology, pharmacology of the toxins, and the main detection methods. Cyanobacteria may produce a wide array of cyanotoxins, being classified, accordingly to the main effects in mammals, hepatotoxins, neurotoxins, cytotoxins, and dermatotoxins. The Baltic Sea being a large brackish water body is heavily eutrophic having severe cyanobacterial blooms with particular emphasis on the species Nodularia spumigena and the toxin nodularin. Palytoxin and its 42-hydroxylated analogue have been found in environmental samples of blooms of the lamentous marine cyanobacterium Trichodesmium spp. obtained in New Caledonia.