Cyanobacteria and their emissions are becoming more widely reported around the world, posing a serious threat to both the environment and human health. Several orders of cyanobacteria have been identi ed to make cyanotoxin, the most common algal toxin. The aim of this research was to develop a method for detecting cylindrosprmopsin and saxitoxin biosynthesis genes in rivers .In November, December 2019 and January2020. Cyanobacteria were isolated from Tigris River freshwater and detected using a compound microscope as well as traditional PCR .All cyanobacteria isolates contained phycocyanin gene fragment.Five isolates of cyanobacteria in these study was successfully ampli ed a phycocyanin gene (Microcystis osaquae, Microcystis sp, anabaena circinalis ,nostoc commune and westiellopsis proli ca) and all isolates successfully ampli ed aoaC gene to detecting the cylidrospemopsin and the saxitoxin. Our ndings show that a PCR assay can be used to detect cylidrospemopsin and saxitoxin-producing cyanobacteria in river water, which is useful for stations that prepare drinking water for the public.