Abstract: Background and Objective: The abundance and distribution of phytoplankton in harbors exhibits spatial and temporal variation. Many biotic and abiotic factors interact to regulate spatial and temporal variations in phytoplankton. This study was carried out to determine which factors can regulate the abundance and community structure of phytoplankton in El Dekhaila Harbor, South-Eastern Mediterranean Sea, Egypt. Materials and Methods: Samples of phytoplankton were gathered during 2012 in El Dekhaila Harbour, for statistical tests three indices were utilized to get the estimation of species diversity (H’), species richness (d) and species evenness (J) and also Pearson’s Correlation Coefficient (r) was utilized for the simple relationship analysis with the variables. Results: Phytoplankton groups were essentially made out of Bacillariophyceae (84.58%) and also, have been determined as the richest group in species variety with 72 taxa. Summer had higher phytoplankton density, however autumn had higher richness and evenness. Skeletonema costatum, Pseudo-nitzschia seriata, Chaetoceros curvisetus and Prorocentrum spp. were frequently recorded. El Dekhaila Harbor suffered of high concentrations of both inorganic nitrogen and dissolved reactive phosphate. Conclusion: Zooplankton grazing activity on phytoplankton may assume a critical factor in regulating the phytoplankton community structure in El Dekhaila Harbor and not the concentrations of nutrient salts or their ratios.