Small, coccoid and rod-shaped Synechococcus-type cyanobacteria with either phycoerythrin or phycocyanin as major accessory pigments were isolated from several large, temperate-zone lakes and the brackish Baltic Sea. The picocyanobacteria had two ribosomal operons with a long internal transcribed spacer (ITS-1) separating the 16S rDNA and 23S rDNA. A 16S rRNA-based phylogenetic analysis assigned all isolates to the picophytoplankton clade [sensu Urbach, E., Scanlan, D. J., Distel, D. L., Waterbury, J. B. & Chisholm, S. W. (1998). J Mol Evol 46, 188–201], which also comprises marine Synechococcus spp. and Prochlorococcus spp. The strains assorted to five paraphyletic clusters each containing two or more strains with 99·4–100 % 16S rRNA sequence identity. Five corresponding strain clusters were deduced from analysis of ITS-1 sequences. Sequence divergence in ITS-1 varied between 23 % in the most divergent and 1 % in the phylogenetically most conserved cluster. Clustered strains with low sequence divergence in ITS-1 were frequently isolated from a single ecosystem or hydrographically comparable lakes in the same region. They represent physiologically distinct ecotypes of species which, among other phenotypic variations, frequently differed in their major accessory pigments, the phycobiliproteins. The reproduction of the various pigment traits in different lineages was not correlated with the phylogenetic divergence deduced from 16S rRNA or ITS-1 sequences but rather seemed to be related to characteristics of the ecosystem and habitat from which the strains were isolated. The occurrence of a comparable spectrum of phenotypes in different lineages and ecosystems indicates that different strain clusters developed similar ecotypes during independent adaptive radiations.