The phytoplankton community was studied in historically and ecologically important area of the Egyptian Mediterranean coast at Alexandria. Once a week sample was collected from a semi-closed basin ;Eastern Harbor,(EH) from June 2011 to May 2012 and twice a week over other one year started from March 2013 till February 2014 at fixed station. The results indicated that a total of 116 phytoplankton species were identified during the first year and 156 species during the second one, with the predominance of diatoms in both two periods (64&100 species respectively) with a percentage frequency 84.23 % and 76.10 % in two periods respectively, followed with dinoflagellates (15.34 % & 23.67 % respectively) . The phytoplankton standing crop amounted to an annual average of 1.84 x 106 cell / l during 2011-2012 and 2.48x106 at 2013 – 2014. C lean differences were observed between the roles of diatoms and dinoflagellates as well as the abundance cycle of total phytoplankton in the two periods. Generally, during the second period high counts of dinoflagellates particularly in 12 of August 2013 cause fish mortality. Eutrophication in the study area was accompanied by more frequent algal blooms, which were sometimes dominated by toxic species. Correlation coefficient of biological factors with some physicochemical parameters are provided and discussed.