Aphanizomenon Morren is an important member of the cyanobacterial community in the Baltic Sea, but studies of this genus have been hampered by the difficulty of growing it in laboratory culture. PCR amplification of DNA from colonies picked directly from water samples has circumvented this problem and made it possible to carry out an analysis of genetic diversity within the Baltic Sea and in two small North American lakes separated by just a few kilometers. The nucleotide sequence of the phycocyanin intergenic spacer and partial flanking coding regions of cpcB and cpcA was determined for 32 colonies of Aphanizomenon, 26 from the Baltic Sea, and 6 from the North American lakes. No variation was detected among the 26 Baltic Sea colonies, but two alleles, differing at 19 nucleotide positions (5.4%), were found in the North American lake colonies. Surprisingly, the two North American types were less closely related to each other than to the Baltic Sea genotype. The Baltic Sea Aphanizomenon is clearly distinct from A. flos-aquae at both the cpcB–cpcA and 16S rDNA loci, which lends phylogenetic support to their tentative separation based on ultrastructural analysis. We conclude that although there is significant genetic diversity in the genus Aphanizomenon, the population in the Baltic Sea is, in contrast to the Nodularia population, genetically homogeneous.