Non-heterocystous, mostly filamentous cyanobacteria were isolated from the crust of stones, from the periphyton of two macrophytes from the littoral zone and from the pelagic environment of Lake Constance. All isolates were cultivated as unialgal strains. DNA analysis by restriction fragment length polymorphism with the psbA gene probe revealed high genetic diversity among the strains from the littoral zone. For all genotypes, the occurrence of the nifH gene encoding a nitrogenase subunit and of genes encoding subunits of phycoerythrin and phycocyanin were tested by Southern blot hybridization. In addition, the isolates were investigated for their ability for complementary chromatic adaptation (CCA) and for anaerobic N2-fixation. With respect to these characteristics, all cyanobacteria included in this study were assigned to four different types: (1) strains without the capability to fix N2 or to perform CCA of the group III type (CCA III); (2) strains which show both features; (3) strains with the ability to fix nitrogen, but that do not show any CCA III; and (4) strains that produce phycoerythrin, but without the capacity for CCA III or N2-fixation. By examining the frequency distribution of isolates, these types were shown to prefer different habitats. While cyanobacterial strains capable of N2-fixation, but without CCA III, were mainly obtained from stone crusts in the supralittoral zone, those with the potential for N2-fixation as well as for CCA III were largely isolated from submersed macrophytes. Cyanobacteria that produce phycoerythrin, but do not perform CCA III or N2-fixation, were found in the pelagic zone only.