Cyanobacterial community of Akgol Lake (Terme, Samsun) was analysed to determine both their contribution to bacterial biodiversity and representation of toxigenic members with a metagenomics approach. Sequences obtained from the amplicon of V3-V4 regions of 16S rRNA gene revealed that cyanobacterial sequences consisted of 0,35% of total bacterial community sequences only indicating a little contribution to total bacterial biodiversity. Monthly scanned sequences of the parts of cyanobacterial 16S rRNA, Microcystis spp. 16S rRNA, rpoC1 and cpcBA genes showed that cyanobacterial cells were detected only in late spring, summer and early autumn. According to the cloned and randomly selected sequences of rpoC1 and cpcBA regions, most of the sequences were closely related to Microcystis aeruginosa. Although a total of 9 cyanotoxin gene regions were scanned using specific primer pairs only 2 amplicons, mcyB and mcyD of Microcystis spp, were detected through the cyanobacterial representation period of the year. Sequence analyses of cloned mycB gene showed that all the sequences were clustered with Microcystis aeruginosa mcyB gene. Therefore, results of this study indicates that toxigenic and/or non-toxigenic cyanobacterial individuals were represented in the water column of Akgol Lake even they are not abundant among bacterial community members.