In the present study, the cyanobacterial flora of Urmia Lake (NW Iran), one of the largest salt lakes in the world and adjacent rivers is investigated. Urmia Lake comprises different micro-organisms including cyanobacteria which have a major role in aquatic ecosystems. Cyanobacterial samples were collected in 2008–09 from Urmia Lake and its surrounding ecosystems. All samples were cultivated, isolated and identified using morphological keys basically and also molecular methods via 16S rRNA sequencing in some cases. Following cyanobacterial species were isolated from Urmia Lake: Spirulina maxima, Gloeocapsa sp., Oscillatoriasp., Nodularia spumigena, Phormidium fragile, Oscillatoria salina, Plectonema notatum, Aphanocapsa grevillei, Trichormus variabilis, Lyngbya sp., Phormidium sp., Microcoleus chthonoplastes, Leptolyngbyasp., Chroococcus turgidus, Microcoleus sp., Chroococcus dispersus, Nodularia sp. and Nostoc sp.. These variations may be referred to limited sampling, or increased salinity of the lake during recent years that has eliminated some non-tolerant species. This study reflects the biologically activation of Urmia Lake despite the hypersalinity and extreme condition of it.