Geographic expansion of toxic cyanobacteria is a serious threat to aquatic ecosystems. The detection and accurate identification of harmful cyanobacterial species is essential for monitoring the distribution and expansion of potential bloom formers. Molecular approaches are particularly useful due to the ability of these techniques to differentiate strains and detect HAB species at low densities. These approaches have been applied to two river systems with a history of cyanobacterial blooms. In the eutrophying, N-limited Neuse River Estuary, NC, USA, cyanobacterial species capable of N2 fixation may be periodically selected for bloom formation. The spatial and temporal distribution of the N2 fixing cyanobacterial population of the Neuse River Estuary was mapped by detecting the nifH gene, which encodes nitrogenase, through PCR. The nifH gene, and thus the genetic potential for these cyanobacterial bloom formers, was found to be present throughout the Neuse River Estuary during most of the year. Sequencing these PCR products revealed potentially toxic Anabaena sp. and Anabaenopsis sp. to be the most common nitrogen fixing cyanobacteria present. Deteriorating water quality due to harmful cyanobacterial proliferation also plagues the St. John\'s River System, FL, USA, which supplies drinking, irrigation and recreational waters for approximately 3 million people. The cyanobacterial community of the lakes in this river system was characterized using nifH and 16S rRNA. Molecular probes based on the DNA (nifH) sequences of toxic species can differentiate these from non-toxic strains. Identification of toxic cyanobacterial species at low densities is critical to permit management actions before these species reach bloom proportions.