The assessment of the phytoplankton community structure in the Bitter Lakes during 2012-2013 indicated about 150 species belonging to 73 genera. These are classified as 89 species of diatoms, 27 dinoflagellates, 19 chlorophytes, 13 cyanophytes, and one of euglenophytes as well as one rare species of silicoflagellates. Diatoms were the leading and most dominant group forming about 81.67 % of the total number of individuals due to the high flourishing of Rhizosolenia alata variety gracillima, Thalassionema nitzschioides, Skeletonema costatum, Thalassiothrix frauenfeldii, and Chaetoceros lorenzianus. AbuRommanh was the most productive area in the phytoplankton counts, whereas the area of Shandoura was the lowest productive one, coincided principally with the types and amounts of pollutants as well as the highest human and fishing activities at this area of the Bitter Lakes.