Between the summers of 2005 and 2007, studies have been conducted for five seasons in several marsh locations in southern Iraq. During five surveys, 317 taxa of phytoplankton belonging to six major groups were identified. These included: 204 taxa of Bacillariophyceae (represented by 13 Centrales and 191 Pennales, thus 14% and 27% respectively of all taxa recorded), 59 Chlorophyta (28%), one Cryptophyta (4%), 39 Cyanophyta (21%), 10 Euglenophyta (2%) and four Pyrrophyta (4% of all the taxa recorded). The Central Marsh, Hammar Marsh and the Hawizeh Marsh had higher phytoplankton populations compared to all other studied sites. The dominant phytoplankton groups throughout the study area were the Bacillariophyceae, Chlorophyta and Cyanophyta. The dominant species were Cyclotella meneghiniana, Kirchneriella irregularis and Nitzschia palea. A progression in the richness and biodiversity of species occurred during winter. These three phytoplankton groups were dominant in waters of southern Iraq and were responsible for most of the species richness and diversity observed. Generally, sites changed from summer to winter according to the changing conditions associated with nutrients, salinity, temperature, and light intensity. These controlling factors influenced phytoplankton biomass from season to season.