Blooms of Cylindrospermopsis raciborskii and Anabaena spiroides were studied in relation to their toxins composition, geographical locations, and other characteristics of the waters in the southern region of Brazil. All forms of Cylindrospermopsis were paralytic shellfish toxin producers, with a similar profile of the toxins. Anabaena blooms were studied in relation to the production of anatoxin-a(S). In all samples containing Anabaena spiroides, a positive result was found when the AChE inhibition technique was used. Methods applied for both studies are very convenient for monitoring this large region and give a reasonable view of the present situation of water reservoirs in southern Brazil.