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Cyanobacteria and their toxins are an emerging water quality issue for providers of drinking water and managers of waters used for recreational purposes. Robust and sensitive analytical methods are required for monitoring toxins and assessing their behavior during water treatment. This paper reviews the toxins produced by cyanobacteria (cyanotoxins) that include: neurotoxins (anatoxins and saxitoxins [paralytic shellfish poisons]); peptide hepatotoxins (microcystins and nodularin); cylindrospermopsin; and, lipopolysaccharide (LPS) endotoxins. The methods currently available for their analysis include: extraction procedures; concentration/cleanup procedures; sample preservation; and, determination of anatoxins. Includes references.