The genetic diversity of cyanobacterial communities was studied at various depths in Lake Kinneret (Israel). Denaturing gradient gel electrophoresis (DGGE) of specific 16S rRNA gene PCR products showed significant differences in the cyanobacterial community structure between epi- and hypolimnetic waters. Sequences of clone libraries prepared from 16S rRNA gene PCR products from epi- and,hypolimnion revealed the presence of at least 11 different groups of cyanobacteria. Clones related to the unicellular cyanobacteria (Chroococcales and picocyanobacteria) dominated the clone libraries from both depths. New primers to amplify the gene coding for the photosystem 11 reaction centre (psbA) and the nitrogen regulator gene (ntcA) of cyanobacteria were developed and used for further characterization of the cyanobacterial communities from the lake. Sequences of psbA amplicons clustered with those from 2 different groups of marine Synechococcus and Chroococcales. Cloned ntcA amplicons from the lake were closely related and did not cluster with sequences from cultured cyanobacteria or other environmental sequences from this gene. All the molecular markers analyzed here showed similarity to sequences from some groups of cyanobacteria in the lake and those so far found in marine habitats.