Cyanobacteria as the first photosynthetic organisms of planet earth are made it habitable for its residents. They are able to tolerate extreme environmental conditions. Secondary metabolites of cyanobacteria are key factors that make them able to survive in such environments. Some of these secondary metabolites are considered and under investigation for utilizing in biotechnology. Cyanotoxins are among cyanobacterial secondary metabolites which are detrimental and, in some cases, vital for the life of human and animals and according to international standards they should not pass more than a limited defined amount. Thus, no research has done about cyanobacterial toxins in the Shastfich river of Baft city of Kerman province of Iran before and this research is the first attempt to find cyanobacterial toxins by PCR approach for this site. In the present study, we investigated the cyanobacterial flora of Kalenjir region in Shastfich river of Baft. Iran. After sampling and treating them by BG11 medium they identified microscopically using valid international keys. Two genera identified as potentially toxic so in order to identify toxic strains, PCR based microcystin detection has carried out which lead to no band on an electrophoresis agarose gel. The strains of toxic and non-toxic cyanobacteria can be present in one place and compete ecologically and each of them survives and be dominant by the aid of their favorite environmental factor. To conclude, it is suggested to examine the presence of nodularin and cylindrospermopsin gene clusters in cyanobacteria of this region and measurement the amounts of mentioned toxins in water throughout a year.