In this study, surface water samples were collected monthly from five stations inclduing Nayband Bay, Assaloye, Dayer, Kabgan and Bushehr from December 2012 to June 2013. Sampling stations were chosen according to data being collected during algal bloom caused by Cochlodinium polykrikoides in 2008. A total of 45 genera of phytoplankton belongs to four classes were totally identified accounting for 53 species of Bacilariophyceae, 32 species of Dinophyceae, one genus of Euglenophyceae, and one genus of Cyanophyceae. Bacilariophyceae with 89.5% was the most abundant family followed by Dinophyceae with 9.03%, Cyanophyceae with 1.25 % and Euglenophyceae with 0.22 %, respectively. The highest phytoplankton abundance was observed in Bushehr and Nayband Bay stations. In addition to statistical tests, Shannon (Shanon-Winner) and dominance indices were investigated. The lowest variability for Shannon index (1.90) was recorded in Bushehr Station in comparison with other stations. The highest Shanon index was in Dayer station (2.90) with the increase of diversity in Dinophyceae. Evidence of coastal pollution in Dayer along with nutrient inputs from land might be effective in increasing the Shannon index. At 80-90% simmilarity, the results of Cluster analysis separated Dayer station from other stations. It seems that a part of uniformity in phytoplankton abundance is affected by the mild conditions of ambient temperature. The total diversity of phytoplankton in the study area was low. The relative moderation of temperature seems to have contributed to the dominance of diatoms. Yet, the increased volume dust (as emerged by the increased dusty days per year) and the introduction of its accumulation in the Persian Gulf waters, along with other pollutants on phytoplankton communities might be underlaying factors for the dominace of diatoms in the study area