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Phytoplankton study has become more significant in the Caspian Sea due to the occurrence of ecological events such as algal blooms and the introduction of the invader species (Ctenophore, Mnemiopsis leidyi). A seasonal study was conducted to investigate the features of phytoplankton community one decade after this invasion in the Iranian coast of Caspian Sea during 2009-2010. According to the results, 195 species in eight phyla of phytoplanktons were identified. In spring, Bacillariophyta and Pyrrophyta were the dominant phyla with 40 and 29% of total abundance, respectively. In summer and winter the dominant phyla were made by Cyanophyta (92%) and Bacillariophyta (94%), respectively. The Bacillariophyta (57%) and Cyanophyta (28%) were the first and second dominant phyla in autumn. It seems that the ctenophore invasion into the Caspian Sea (due to the changes in nutrient levels and decline of phytoplankton grazers) and human’s destructive activities play an effective role on phytoplankton community during the period. These changes were mainly accompanied with appearance of new and harmful species (with the ability of severe bloom making) and consequently, displacement of native species in this semi-enclosed ecosystem.