Several cyanobacterial species can produce powerful toxins that provide a serious threat for water quality, other aquatic organisms, and human health. These harmful cyanobacteria are especially prominent in freshwater ecosystems, and are a major concern for water managers. Owing to the scientific revolution in genomics, new molecular techniques have been developed that enable the detection of toxic cyanobacteria at a very early stage. New laboratory culture techniques have enabled eco-physiological studies of toxin production at a detailed scale that was beyond reach until recently. Remote sensing of freshwater cyanobacteria is a rapidly expanding field, owing to the increased spectral resolution of airborne data. New computational techniques have led to advanced models on the population dynamics of cyanobacteria. From a management perspective, recognition of the toxins produced by harmful cyanobacteria has recently led to new environmental policies with respect to toxic cyanobacteria in many western countries