Abstract:In the period of February-May 2012, harmful algal blooms (HABs) along with environmental factors were investigated biweekly in the Golden Horn Estuary at the northeast of the Sea of Marmara and a dense bloom of the raphidophyceaen Heterosigma akashiwo (Y.Hada) Y.Hada ex Y.Hara & M.Chihara was observed in late May. H. akashiwo abundance increased gradually from the lower estuary to the upper estuary. The dense bloom of H. akashiwo in late May occurred at the temperature of 20.2°C and salinity of 16.4 psu and its abundance reached to 10.4×10 6 cells L -1 . When compared to mid-May, the mean temperature of surface water increased 4.50°C, while salinity decreased 2.30 psu in late May. Secchi depth values decreased rapidly from the lower to the upper estuary (6.00 m to 0.50 m). It is considered that a rapid increase in temperature, a decrease in salinity, and high nutrient concentrations in combination with low water circulation at the upper estuary were the causes of the bloom of H. akashiwo. Fish mortality or other harmful effects in environment were not observed during the H. akashiwo bloom. But, these events may create a potentially toxic risk for the study area in the future.