Bloom-forming toxigenic cyanobacteria occur worldwide and some species such as Microcystis aeruginosa and Anabaena circinalis, are a particular problem in Australia. There appears to be variation in the strains of known toxigenic species in various regions. One recent study has shown that genetic variation of strains within one region may be limited (Nodularia in Australia, Bolch et al. 1999). However, between regions, other studies show genetic divergence of strains (Neilan et al. 1995, Bolch et al. 1996, Neilan et al. 1997). This study focuses on a molecular analysis of cyanobacterial blooms at one site, in the New England region of Australia. Genetic variation was determined by examination of the intergenic spacer region (IGS) of the b and a-phycocyanin subunits. We have shown that it is possible to routinely obtain template for DNA amplification (PCR), and differentiate the strains in bloom samples. Differentiation was either by restriction endonuclease digestion of the IGS (restriction fragment length polymorphism [RFLP]) or sequencing. Different strains of the one morphotype have been identified within the one site.