Shallow alkaline saline lakes are often found in the Brazilian Pantanal and although their extreme conditions are adverse to many phytoplankton organisms, they may support growth of dense cyanobacterial blooms. Here, we tested the hypothesis of reduced cyanobacterial diversity in these stressful environments, investigating changes between rainy and dry periods and analyzed which methodology would be best suited to assess this community. The cyanobacteria were studied in three lakes at three time periods, using morphological (microscopy) and molecular approaches (DGGE and ARDRA analyses of 16S rRNA gene segments). All methods showed that cyanobacteria dominance was higher during dry periods, probably as a consequence of intensified selective pressure by the increased solute concentration. Anabaenopsis elenikinii was the major bloom-forming cyanobacterium, followed by Arthrospira platensis. Interestingly, these two species never coexisted, but differentiated stages of one were observed during dominance of the other, suggesting that they may be excluding competitors. These life-stage differences, only detected through microscopic examination, show the importance of this approach. However, the detection of small-unseen picocyanobacteria and mainly the possibility to access population genotype diversity reinforce the relevance of molecular techniques. Therefore, this polyphasic methodology was particularly suitable to assess cyanobacteria communities in these extreme environments.