Cyanobacteria is known to form harmful blooms in fresh and brackish waters and also marine environments. Cyanobacteria blooms generally are the indicators of eutrophication in freshwaters as well as estuaries and marine ecosystems. European Environmental Agency rated the eutrophication in the Black Sea as highest concern in 1995. Since the Turkish coastline is also under the pollution risk, the present study was conducted to investigate whether toxic cyanobacteria were present and pose any risk hazard. Samples were taken in five sites along the Turkish coast between Igneada to Samsun, ca 928.5 km long between May October 2012 to investigate the potential of toxic cyanobacteria presence. Twenty eight samples from surface waters were analysed using 16S rRNA and sixteen of them were positive. Cyanobacteria was detected every sampling date in Sakarya river vicinity both microscopically and PCR method. BEP-PCR was used to detect the toxin genes and four samples gave positive results. In contrast, no hepatotoxin was detected with ELISA.