Comprehensive data are presented on the species composition, seasonal and interannual abundance of diatoms and dinoflagellates, trends in the abundance of potentially harmful microalgae in relation to the physical and chemical parameters that affect abundance and distribution from April 2006 through April 2011 from a single location in the Bay of Bandar Khayran (BK). In addition, the spatial and temporal variability of phytoplankton in Bandar Khayran bay as an enclosed ecosystem was compared to offshore waters (OFF) of Muscat as an open ecosystem. Moreover, the temporal variability in sizefractionation of a natural phytoplankton population was investigated to estimate the relative contribution of the different size classes to the overall phytoplankton community and their relationship to environmental conditions. A total of 278 dinoflagellate and diatom taxa were recorded during the study. The Dinophyceae contributed the highest number of species (166) followed by Bacillariophyceae (112). The number of genera present was largest during the Southwest Monsoon (SWM) followed by the Northeast Monsoon (NEM) and lowest during the Spring Intermonsoon (SPIM) with considerable interannual variability. Dinoflagellates were the most important group in the Bay of Bandar Khayran. They constituted 59.7 % of the total species identified in the Bay and dominated the total phytoplankton population most of the year. During the study period, they comprised 83% of the total abundance and 88 % of the total biomass. Diatoms were the second important group and contributed 40.3 % to the total species identified in the Bay. They comprised only 17% of the total abundance and only 11 % of the total biomass during the study period. Diatoms were observed in countable numbers only during 2006 and 2010. Higher abundances of diatoms were observed during February March and AugustSeptember (NEM and SWM respectively) when higher input of nutrients were noticed. Chlorophyll a (Chl a) was associated with diatoms and diatoms were dependent on silicate concentrations. Increases in diatom abundance and their association with phosphate, ammonia and silicate were coupled primarily with a decrease in temperature. Also a weak association was found between dinoflagellate species (except Noctiluca scintillans) and nutrients. The dinoflagellate assemblages that dominated the sampling periods and persisted annually were those in the 15-55 um size range: Prorocentrum minimum, Gymnodinium sp., Scrippsiella trochoidea, Gymnodinium simplex and Prorocentrum micans. This implies a minor effect of grazing pressure on these species. In total, 24 potentially harmful algal species were identified, including 11 species of dinoflagellates and eight species of diatoms. The dinoflagellates Prorocentrum minimum , Scrippsiella trochoidea, and Noctiluca scintillans were most abundant during the Southwest Monsoon (SWM, July-September) and Northeast Monsoon (NEM, January-March) seasons, while other species occurred in low abundance and with no clear seasonal patterns. A dense bloom of Cochlodinium polykrikoides that affected the distribution and abundance of other harmful algal species (HABs) was observed for the first time in the Sea of Oman during 2008-2009. Prorocentrum minimum increased in abundance during and after the decay of the Cochlodinium bloom while S. trochoidea was suppressed during this bloom, increasing thereafter once again. Noctiluca scintillans disappeared in the late SWM and NEM of 2008 and SWM of 2009, when blooms typically occur annually. Prorocentrum minimum and S. trochoidea persisted throughout the annual cycle of all years, enhancing their capability to bloom in the region under favorable conditions of high light intensities, and relatively warm waters of low turbulence. Phytoplankton communities at both at BK and OFF stations showed no significant differences in phytoplankton community composition. However, higher chlorophyll a concentrations and phytoplankton abundance were observed inside BK than in the OFF station during SWM and NEM seasons. This was related to the Bay's unique hydrographic conditions and possibly due to the reduced grazing pressure. Phytoplankton communities at both locations were dominated by dinoflagellates. Despite that, diatom abundance was not significantly different between BK and OFF; it was found that certain taxa dominating each station are spatially and temporally different. Nanoplankton was the most important class contributing 54.4% to total Chla (range 6-82%). Their seasonal highest concentration was during the cold periods when temperature ranged from 28-29 °C in SWM and near 24 °C in the NEM when the supply of nutrients was sufficient to sustain their growth. Picoplankton occupied the second level of the contribution, comprising 23.5%, range 4-74 % of the total Chl a, and their concentration was generally constant (0.04-06 ug L-?) throughout the study periods. A drop in the picoplankton population coincided with increases in the microplankton and nanoplankton populations indicating a high grazing pressure exerted on the picoplankton population. The microplankton size-class occupied the third level of the contribution comprising 22.2%, range 3-65 %. Their general concentration was below 0.1 ug Land only dominant when temperatures were lowest and nitrate, nitrite, silicate and phosphate concentrations were highest. Although Bandar Khayran is located at the limit of the tropical range, its shows temperate dynamics, seasonal temperature fluctuations, spring and summer phytoplankton blooms and high diversity. The Southwest and Northeast Monsoons provide the proper environmental factors for the bloom occurrences and Phytoplankton abundances.