Changes in abundance and biomass of cyanobacteria have been studied in the southern part of the Caspian Sea (the stretch between Tonekabon and Amirabad) in four seasons (spring, summer, autumn, winter) in which samples were taken from five depths of 5, 10, 20, 50 and 100 meters in the stations of Tonekabon, Noushahr, Babolsar and Amirabad. Samples were fixed in formalin (2-2.5%) before transferring to the lab for both qualitative and quantitative analyses. Ten species of cyanobacteria were identified with higher abundance and biomass in the euphotic layer compared to the aphotic layer. Temperature and nutrients have shown significant differences (p < 0.05) in different seasons after normalizing the data through the T-test. On the basis of T test on normalized dates differences were meaningful between population of Cyanobacteria in the optical and no optical layers. Statistical analyses have shown significant and positive correlations between abundance and biomass with parameters like temperature, ammonium and phosphate while it was significantly negative for nitrates.