The investigation on microcystin topics is increasing due to the related ecological and public health risks. Recent investigation confirms a gap in establishing global patterns relating a particular environment to the bloom occurrence of a species and the production of certain microcystin variants. All the results concerning the environmental effects on the microcystin synthesis of one species must be checked in the light of genome diversity. Thus, the poisoning risks of a bloom depend on the strain causing toxicity. To be more effective, specific water treatment methods are required for blooms of different microcystin producing species (such as colonial and filamentous cyanobacteria found in stratified and unstratified water bodies, respectively). With the increasing number of new microcystin variants discovered, the development of new rapid, inexpensive and sensitive enough monitoring methods to promptly screen simultaneously a great diversity of toxins and also check their toxic effects is becoming necessary.