Water environment eutrophication increases the risk of harmful bloom development, like cyanobacterial blooms, which can produce potent toxins able to affect public and animal health. More than 50% of the cyanobacterial proliferation are toxic. Both toxigenic (toxin producers) and non-toxigenic strains, may exist within a single specie of cyanobacteria. It is very important to develop different methods to detect and quantify cyanobacteria and theirs toxins. Although mouse bioassay has been usually used for toxicity testing for cyanobacterial toxins from suspicious samples, actually is being replaced by different in vitro assays that show efficient results. Advancements in immunoassay and biochemical techniques are providing rapid toxins detection methods. Even, several commercial and non commercial kits are available. One of the more promising methods consists of developing molecular probes that recognise DNA or RNA unique sequences to a given species, or single toxigenic strains. All these methods will allow to preview the development of cyanobacterial blooms and their toxins. Also, they contribute to develop studies of control and monitoring.