Chromista and Protozoa ranked the 2 nd dominant group in the study area represent together 16.1 % of the total zooplankton with annual average of 1440 organisms/m 3 and expressed by 69 species. Distinct differences that appeared in the dynamics, patterns of occurrence and numbers of the species in these locations were attributed to differences in physical and chemical conditions.Several environmental conditions appear to control the regional and seasonal distribution of such organisms. Ballast water plays an important role in species mechanical transmission through shipping movements. In conclusion, the community composition of the two phyla and their significant dominance indicated that, El-Mex Bay is a highly eutrophic system which shows signs of partial pollution. Accordingly, it is recommended that the waste water should be treated and/ or recycled before discharge into this natural aquatic system. It was important to produce monograph inside this work containing the photos of the organisms.